Is there a maximum amount of ships you can have in a colony? The rules seem to skirt this issue, everything else in the game has a limit of 4.

There is no limit to how many ships a player may have on a planet (and therefore, form a colony). It is quite common after someone plays a Mobius Tubes late in the game for people to only have a few colonies to return to, and therefore must load 8 or 9 ships onto a single colony.

Several aliens actually benefit or experience this notion on a regular basis: Macron defending a planet with lots of ships is nigh undefeatable; when Amoeba oozes in 8-10 ships and wins on offense, he must land all of those ships on the newly colonized planet.