<t> So I did some tests I found out:<br/>
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-When freighters pick up and drop off resources on mining stations they pay tax. I don't know the exact percentage, but I see a +1k to +2k per tick of bonus income for 62 freighters of mixed sizes.<br/>
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-The same goes for spaceports. The ...

Other than space ports producing and retrofitting private ships, where does bonus income come from?

Cause I still have bonus income after destroying all my spaceports

The corporate tax goes directly to you, it is included in the sales tax. You can see this in the cashflow overview if you set the sales tax to 0%.
The overview tab shows the total corporate tax paid, you can see the real time corporate tax in the corporate control tab under the zone tab.

Corporate tax is levied by the government included in the sales tax.