My experiences with that bonus tell me it is hard-coded....I have 2 reasons for this belief....
1) In my mod I have a planet bonus density of 1...space ponies does not seem any more prominent...Goa has essentially confirmed this with his mod as well...now to be fair, I haven't done a legit analysis of this so it may just be in both cases that it is "rare enough" where you can't distinguish a difference without actually counting it and doing the math....
2) Removing the space ponies planet bonus from the entity manifest can cause minidumps...it is entirely random and not particularly likely, but it can happen both when trying to start a new game and when trying to run sins at all...this tells me that any map that tries to spawn space ponies (including the frontend galaxy on the main menu) when it is removed from the manifest will cause a minidump...of course, if space ponies is removed from the entity manifest and the GSD and any planet entities, the only way the game would try and spawn it is if it is hardcoded....
Thus, I am fairly certain space ponies is hardcoded....the only thing you can really do force it to spawn on certain planets using the GSD or the planet entity files...