This idea does come up a fair bit. The reason it's not in the game, well... let's take a look at what ships would be prime candidates for it, conceptually.
Anything with lots of front-facing firepower is a decent match at first glance. So, the Dominator, the Onslaught, maybe the Hammerhead/Eagle/Falcon. Perhaps a few other ships. Note that most of these (all the ones listed, at any rate) already have front shields. Combined with frontal-focused firepower and engines being in the back, it's already a great idea to flank them.
So, gameplay wise, what would this actually change? It'd either make the ships tougher from the front (which you could easily do within the existing framework by adjusting the shield stats) or make them even more vulnerable from the back (which isn't a good thing - they're already very vulnerable.
To top it off, ships aren't exactly like tanks. They're more like, well, ships. The nature of the combat means that hits to the back are at least as likely as hits to the front in anything other than a 1-1. A ship designer would probably go through great pains to make the engine section of a front-shielded ship as durable as possible - that's the Achilles heel of a large ship, after all.
The current system serves its role - rewarding surgical fire my making repeated hits to the same area more effective. Varying armor by location... well, I'm not going to say it would flat out be a bad thing. But at the same time, I don't see what compelling gameplay it brings to the table, and it does bring complexity. All this information would have to be conveyed to the player somehow.