I'd say habitats are excellent for manufacturing, freeing up building slots on your other planets for more important things.
I tend to go with a 4 house - 4 trade district split on them most of the time. If M income isn't an issue, 5-3 works as well - that allows you to fill all building slots, but you'll need several maxed out alloy or CG factories to employ pops.
They are also pretty decent for science. Each district equals a T2 lab, so the initial alloy upkeep is compensated for rather quickly, but I actually haven't used them much in that capacity, since my planets are usually used for science and I tend to get more than enough from them.
A thing I am currently experimenting with is using them for naval capacity. Strongholds are a bit weak as a building, but building slots is what Habitats are all about. Problem is, you'll either need some other buildings to employ the leftovers OR use less housing (3-5 or even 2-5 split).
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This thing costs 5 alloys + 1 mote and provides 11 soldier jobs for a total of +44 naval capacity and a ton of trade value to pay for its upkeep. It also comes with an FTL inhibitor and 50 defence armies, a formidable bulwark. I'd say it is actually more effective at denying enemy fleets passage than a citadel, particularly once jumpdrives enter the field. During war you can just swap out the Stock Exchange for a Shield Generator to make it even more annoying to deal with (also great synegy with the 25% bombing damage reduction from Adaptability!). You can, of course, make the whole thing even more insane if you use more housing districts and either accept the unemployment or put down a few alloy plants.
I did something similar but staffed the station with battle thralls to double as a recruitment center. Can the military academy be built on a habitat?