It's probably best to (dis)allow them on a case-by-case basis. Align weapon, keen edge, (greater) magic weapon, and weapon of impact seem fine, since they can't stack with similar effects. Weapon of energy might be too much since it explicitly *can* stack with the emulated weapon property and could arguably stack with different damage types of itself (i.e. have the acid, cold, electricity, and fire version of weapon of energy on the same weapon at the same time). Sonic weapon is anyone's guess: while all of the other spells explicitly state whether they do or do not stack with the emulated weapon ability, sonic weapon doesn't. I'd probably leave it out just for being ambiguous.