Changing PI's (from B+ to 3). Will site ID stay

Yes.
The Station number is no more linked to Pi’s mac address. It is now linked to feeder-id also known as UUID (unique user id).

As the feeder-id (UUID) is saved in the card, your Site number should be preserved when you change the Pi, but use same card.

However in unlikely case of not getting back same Site number by default, you can still get it back manually by method given here:

For Begginers - How to Get Back Existing Station Number in A Fresh Install