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So I was thinking about a ship scale mod for Space Empires IV I used to play that also had some interesting ship designs, eg a massive rail gun mount that ran almost the length of the ship. That kind of thing.

So if you look at the US Navy a Battleship is about 5-10 times the tonnage of a Destroyer.

In Distant Worlds 2 a Battleship is twice the tonnage of a Destroyer. Roughly speaking if you took a destroyer and increased each of the three dimensions by a bit over 25% you would get a destroyer. On the actual map a (Hakkonish, since that's what I'm currently struggling through) Destroyer looks like it would need to be 50% bigger in every direction to be the same size as a Battleship, which would SUGGEST a Battleship is over 3x the tonnage of a Destroyer. I think these are still rookie numbers.

Destroyer 600t, Battleship 1200t. The Battleship has twice the volume of the Destroyer.

Destroyer 4 defence slots, 5 weapon slots. The Battleship has 10 defence slots and 12 weapon slots.

I'm starting to see a problem here. The Battleship brings bigger weapons to the fight so you would expect 12 weapon slots to take up more than 2.4 times the weight of the destroyer weapon slots.

Now, neither the Battleship or the Destroyer is likely to be maximising the tonnage of weapons carried but even so it seems like a discrepancy.

You see what I'm getting at? Tonnage equates to volume. Double the volume of a destroyer and you increase the surface area by, I want to say 40% but I'm winging it a bit. That's why I need a smart person. If I'm increasing the surface by 40% how am I getting 2.5x the defensive slots?

Anyway, I'm 100% happy to be told I'm wrong, but my main point is the way ships are handled is pedestrian, at best. Keep all the stats but make each upgraded ship size significantly bigger and heavier. Introduce slot sizes for shields and armour to account for the greater surface area. XL Shields? Sure, why not.

And, especially, have a big long ship with a massive rail gun that runs the length of it so you can properly tilt at windmills.

I believe you are thinking too much about a water based navy ship and not fully considering what a 'space based 'navy' would look like. Water based battleships had to be big to support the weight of their weapons systems. If it were possible to put 16 inch guns on a destroyer, they would have. In space, weight is much less of a concern as there is no gravity, and the weapons systems mass is in no danger of 'sinking' the vessel.

Also, consider crew size. A WWII battleship had over 1000 crew members, and they needed accommodations. Today's cruisers are only marginally larger than a destroyer, yet have a much smaller crew size that their WWII counter parts. What automation a space warship would have, that's subjective, but I imagine technology to be so advanced that much less crew would be needed, therefore requiring much less of a hull size.

As for mega weapons,have a look at the planet destroyer in game. I believe it speaks to you hull size to house a specific weapon.

Awesome question, one which I feel compelled to answer elaborately!

Quick correction to the previous post: Weight matters equally in space, as is excellently simulated in the Kerbal Space Program franchise via thrust-to-weight (effective acceleration), fuel weight combined with fuel efficiency (specific impulse or ISP) and finally calculated as Delta-V (total speed change available given all predictable factors, until refueling). Sinking is replaced by a more specialized emphasis on mobility; tomato tomahto where tonnage is concerned, though dimensions indeed matter less in space (not zero, though, as even space has minute resistance which will matter at speeds required for quick interstellar travel).

I think this answers the OP: When the above constraints are abandoned, sci-fi becomes fantasy. Of course, most mainstream sci-fi and even mainstream pseudoscience such as alternate universe theories are unfalsifiable (fantasy by definition), so you could go that route without alienating a typical audience.

Scale is up for debate as we could imagine exotically dense materials being used in advanced reactor cores, engines and weaponry, for example, or imagine gravity-manipulating devices used to alter materials' properties (at which point we can only shrug). Neutron stars are absurdly dense, and our uncertainty gets worse if we imagine a contained black hole being utilized. In physics we don't know much about black holes except their visible and inferred effects, and we're not sure about the latter.

Either our understanding of material properties hold, or they don't. In the former case, calculating size should be doable after choosing materials and evaluating ability (damage, range, speed etc.), then coarsely inferring what sort of bulk said ability would require. Class designations such as "Destroyer" and "Battleship" are arbitrary, being functional roles rather than real objects. This has no relation to scale or tonnage.

One could have a space station of epic size, which is very different from naval bases, but that's besides the point. Speed limits weight whenever it is desired. This doesn't change if we move from a real gravity-based galaxy to a drag-based galaxy like in DW2, except that in reality, acceleration, the ability to deflect hazardous space dust and evade rogue comets (meaning absurd-range sensors) are more important to getting around than absolute distances due to the conservation of momentum.

Of course, hyperspace/warp is fantasy rather than real sci-fi so it can be whatever the devs want it to be. It's magic. According to Star Trek Discovery, it's potentially mushroom-related and requires the ship to flip upside down... but I digress. Better not open that box of silliness.

In conclusion, you've a great deal of leeway in designing your sci-fi mods, but good sci-fi requires at least some accuracy based on what we currently know. I'd say you're doing fine based on what you wrote.

One thing that the game actually do consider that many don't realize is that thrust to weight ratio is not always a good metric. While it is true that there is a strict correlation between thrust and weight to give you a specific acceleration, what is not always understood is that of internal integrity of the object that thrust is applied to. The more massive an object is the more of that mass must be applied to just keep the structure from ripping apart when thrust is applied to it.

In the game this is symbolized with smaller ship hulls having bonuses to speed for example.

In terms of scale... you can technobabble this in any way you want. There does not have to be a direct translation of the volume and the shape of the hulls or the weight system of the game. The weight system is likely just a subjective metric that is neither volume nor actual mass.
This means that you can have whatever scale you want and then use whatever weight limit you want.