Better if you don't remove the covers, you could damage them in the proses and they are more valuable when they have not been tampered with
Definitely check the current price difference between opened and unopened PAFS so you know how much devaluation will occur.
I think whatever you do mostly depends on your buyer and your need or ability to prove authenticity.
The only reason I can see for opening them is if that is what is needed to make the sale, to satisfy the buyer's concerns, or to clearly photograph the internals to back your self up against any claim of recourse from an unscrupulous buyer.
But provenance like showing the PU's attached to a '59 guitar, or a bill of sale to your dad along with any proof that he died in '65, might also go far to adding confidence with respect to a covered PU (as well as date the PU).
But if you have to open them - I would think opening only 1 would be sufficient and make sense. Whatever you do, do it with utmost care.