Can a 2-card ship (CR-90 or Raider) equip 2 modifications? 1 for the front and 1 for the back? I didn't THINK so but it's letting me do that in one of the squad builders I'm using so I'm now uncertain.

Fairly sure you can't, but it's not 100% clear.

No, the squad builders are wrong.

Page 20 of the Rules Reference says each ship can only have 1 mod. Page 1 of the Huge ship rules says that a Huge ship is still just 1 ship even if it has two ship cards.

Therefore you can only equip one mod on a Huge ship.

The squad builders are mostly wrong due to coding issues because they mistakenly treat the two ship cards of a Huge ship as if they were two separate ships.

Thanks, that's what I thought.

Can a ship equip 2 modifications?

nope

It's a shame really. If you run ordnance you can't run automated protocols.