[ ... ] But generally speaking, it doesn't feel right to take donations for what's ultimately a commercial enterprise [ ... ]
1. Commercialy - many of us thought that the game we bought would entertain us for a few, maybe a dozen hours. In practice it is a common sight to have several dozen, or several hundreads hours clocked in over several iterations of the game, thus felling we got far more than the money's worth. From this perspective, you could also count continued forum replies, commentaries, develeoper feedback, customer support etc. as additional services - 18k posts and counting. It is also a given that more money equals (more-less) less worries, equals more of team's time saved, equals more starsector thingies for us to recive. Commercially sound.
2. Passionately - while starsector is your project, many of us share the passion and enthusiasm for it, and would gladly support it.
3. Practicaly - imo a good Patreon-esque, non intrusive game-wise and developer-control-wise option would be to set "donation bounties" for adding lore-friendly names to capitan name generation tables, or name generation tables for specific ships. Taking all of the above into considerations, i'd gladly throw a nice few bucks to get a chance for "snicka blasterflash" or to have a (rare) chance of encountering Hyperion class ISS "Nothing personal".