Yeah, mines still detonate for cloaked vessels whether the cloak is from device or storm/asteroid etc.
Also, if you launch mines there, it won't blow up any ships they have there - they have to move into the mines for them to work.
Sounds like that planet is giving you some trouble

. I think you need to research sensors that can see at level 17. If you can use Temporal or Pshycic ones it will be cheaper than getting standard Tachyon ones. With them you will be able to see any ships and also the number of mines they have there as well as actually be able to attack the colony. Then attack with mine sweepers escorting your ships. Freighters make good mine sweepers - the sweeper component goes towards the cargo requirement in Balance Mod anyway.