The cloaked ships should show up on the planetary summary sidebar, too, but haven't been since the port to Unity (version 4.0). That's something I really need to get back in the game again.
Glad you're enjoying it -- and yes, it's definitely a big game! It might be that those ships are actually at a stealth guard post, in which case they are actually working as intended. You can always use a tachyon drone or decloaker (SUP menu), or a tachyon warhead (missile silo) if you really want to find those ships.
If they are just hanging out randomly, do be sure to open a mantis issue, but it shouldn't be any sort of bad hangover from an older version of the game or anything. Doesn't mean it isn't, but it shouldn't be!