right so i have the power armour exocraft armed and set up to be basicaly support unit for me whenever i attack random Sentinell presence (mission based so likes of pillar or such.

Due to this i've hit the build limit of 5 per planet, yet as at most one is in a settlement / base i can not realy find them in sensible manner. is there a system that would alow me to remove those bays without having to find them first? it sounds like ripe pain in the bum to even try to find them considering tha planets are big and scanners are only way i cna even phanthom being able to detect having severe limitations in how far they can scan.

While this will not help remove the excess geobays remotely (without finding them) in the future you can delete the geobay immediately after summoning the exocraft and the exocraft remains available and can be summoned using the X (quick menu) key..

There are two additional options:
1. You can build an Orbital Exocraft Materialiser on a freighter and while the freighter is in the same system you can summon exocraft without building a the otherwise necessary geobay.

2. You could also build an Exocraft Summoning Station on a planet which can be used if you have already have buiit the appropriate geobay somewhere in the system.

Good Luck

You could mark their position with a save beacon.