You can reverse-target secondary weapons; I think it's either shift+select or option+select by default on Macs, but I can't check it right now because I'm a dirty traitor and running XP off my Intel iMac at the moment. I'm not sure what it would be if you're on Windows, though, but you may be able to check it in the in-game settings.
There are three ways of getting missiles to fire out the side of the ship. There's the blind spot route that you're looking at, you'll need to use submunitions to get the desired effect. The supermunition will be an unguided turret with the blindspots you mentioned, but they will need to submunition into a guided missile since a weapon can't be both a turret and a missile. I'd recommend giving the turret a life of 1 frame (don't forget not to check the "flack" box as well for the turret) unless you want there to be a longer delay before the guidance kicks in.
The second method is the "roll out," which I haven't experemented with much, but if I remember correctly (did it by accident once), you mark the weapon as guided and set its inaccuracy to -90 degrees. Or maybe it's -180 degrees, I don't recall. Anyways, this will make the missiles travel at an angle perpendicular to the direction you're facing, but the missile's graphic will actually be facing the same direction you were when you launched them (so they are moving sideways in relation to their bearing). I believe they will keep going that direction until their guidance kicks in around 1-2 seconds later, at which point they will start moving in the direction they are facing, which is also the direction you were facing when you launched them. whew
The final method I'm much more familiar with, as I use it extensively in my hypothetical TC. In this one, you again use a submunition, but to achieve a different result. You make the supermunition an unguided shot with count of 1, then make it submunition into two of the given missile, with a sub theta of -90 (or is it -180?) This makes the missiles point and move sideways, as opposed to the "roll out" method, which launches them facing forwards but moving sideways. This final one is my favorite, since unless you give the missiles a really high turn rate compared to their speed, you still need to be smart about launching them. The reason for this is that missiles in Nova have an inescapable 1-2 seconds of being a dummy projectile before they actually lock on to their target and begin homing in, which means that if you're not careful, the missiles will blossom out too far and end up flying circles around your target. Also, it looks pretty as hell, and I've always found beauty in destruction to be a very disturbing yet nearly mesmerizing sepctacle.
One final thing to take note of: every one of these tricks will cause a different exit behavior. With the first, all the missiles will exit the ship on the same side (the side facing the target ship). With the second, they will alternate sides (I think), unless you have multiple platforms and make them fire simultaniously. With the final, they will always fire from both sides simultaniously, since each supermunition turns into two that travel in opposite directions. Also note that with the last one, you should either halve the damage of each missile or double the weight of the supermunition (since each one ammunition turns into two missiles).
OK, sprites vs. spins.
A sprite is a grid of images, each tilted X degrees clockwise of the one before it. Sprites are most commonly used to generate rleDs, which is essentially a movie of a ship or weapon. (Yes I know that you can use sprites and animations for other things too, like a hypergate opening, but I'm keeping it simple for now).
A Spin file takes a sprite or rleD and gives it more attributes, plus it allows the sprite/rleD to be linked to a spob (space object) or weapon animation. Ship animations are far more complex, and therefore use Shans instead of Spins.
That's a very, very rough overview; if you want more information, you can find it in the Bible or probably in one of the various help stickies on this forum. I'm sure someone else will be able to give you a clearer explanation.
Anyways, hope that helps! Best of luck!