Both ways are perfectly justifiable, depending on both the nature of the weapons and what the damage is thought to represent.

If you are thinking of small turrets, and the damage represents severe damage to the turrets, then directionality of the damage matters.

If you are talking about a weapon that is largely internal, direction is irrelevant - you are smashing through about the same amount of hull to get to it from directions it can't fire as ones where it can. For a specific example, see the missile tubes in the Honor Harington books.

If the weapon damage is mostly blown breakers, severed power feeds, and things like that then direction is again not really an issue - power surges can flow around in all sorts of directions, and the power feeds aren't running along the outer hull (at least I hope not).

You have to decide what sort of weapon systems are in use in your setting and what level of damage the hits to them represent before you can make the decision. Also, if you decide that direction does matter then there is a good chance that you will need to decide that Damage Control can't fix weapon hits.

Thanks for all of the replies.  I like the concept that the direction of the attack determines which weapons get destroyed (this is probably how I'll end up playing).  Though that could bring up a situation where there are no weapons left on that facing... in which case I would just go with the general system damage approach and either choose one or make a random roll.