...you'd have to make a choice: Do I want an extra weapon to dish out damage or something that provides some kind of ability that I wouldn't otherwise have?
But I think that is already handled by the whole Ordinance Points system. You can have more weapons, or you can have hullmods that provide bonuses you wouldn't otherwise have. It's the same thing.
That said, I wouldn't mind the ability to place purely cosmetic items in unused weapon slots.
It's not entirely the same thing. You can increase the number of ordinance points via skills, for example, but you can't increase the number of hardpoints. Hull mods could also be expensive in different ways. Perhaps a hull mod costs some OPs and a hardpoint too. That's a lot to pay for a mod, it better be pretty good. Or it might require only a hardpoint and no OPs, so it costs you in a different way than standard hull mods. It's a way to add more diversity and give the player more options.
For example, you can't currently expand your cargo capacity in any way that I know of. It doesn't really make sense to have a skill or a hull mod for that, there's only so much space inside a ship, you can't just magically inflate it. If you want to carry more cargo than fits in your ship, you have to go over capacity, basically strapping the extra stuff to the outside of the ship, and run the risk of an accident as a result. Suppose there was a hardpoint-mountable external cargo container. You could use that to expand your cargo capacity without risking an accident (since it's actually properly attached and not just strapped on with duct tape). The downside is that now you have a cargo container where a gun used to be, and if it gets hit in combat it's going to be destroyed along with everything in it. So it still costs you and there's still risk for carrying more stuff than you should normally be able to, but it's a different kind of risk.
But yeah, I think that unused hardpoints should be automatically covered by some kind of protective cap. You don't want to leave all that machinery exposed