Yes, they count towards your hand limit.
Have you been dumping all of the units at the system where the base is once they change systems? For example if there are a crap ton of units on Yavin 4 and then move to Hoth, the units do NOT go to Hoth. They stay on Yavin 4.
I find having to start fresh makes it easier for the Empire to destroy the base when they find it again. I crushed a player as the Empire once even after they changed their base twice.
Having said all that, a -1 rep each time they change bases is better than a summation loss of rep points.