1. Yea, if the hatch is on the surface and the cage underground, trolls (and other building destroyers) will see the hatch and want to destroy it. You could also exploit this by placing (ideally webbed) cage traps around the hatch, if you want.
2. Don't think they'll try to attack the dogs, if they're in a cage and/or behind a locked hatch.
3. There IS an attacking from behind bonus (or at least I assume so, because why mention attacks from behind in fortress mode combat reports otherwise), but I think it's mostly/only for being shot at from behind. So sending 2 forces at invaders from different directions will give minimal benefits, if any, in terms of combat rolls, but of course you'll surround them faster, and they'll have a hard time running away, so the tactical advantage still remains.
And, as noted, a lot of the dogs will die; they're unarmored, and smaller than a dwarf/goblin anyway.
3.1. Yes, because a) they'll be hitting the dogs rather than shooting railguns crossbows at your dwarves, and b) a crossbow isn't a proper hammer in melee, nor is a bow a very good sword (bows use sword skill in melee IIRC). Neither are harmless if made of metal, but not as dangerous as the actual weapons either.
3.2. Line of sight, so no doors/walls etc, and a distance of what, within 20 tiles or so? Thereabouts, anyway (compare to how close invaders need to get to stationed military before said military notices them and charges at them).
4. 50 dogs per cage is fine if you want to do that. There's no delay on leaving the cage, but they might take a few extra seconds all squeezing through the 1 ramp tile, much like dwarves squeeze past each other in 1-tile wide hallways. Probably wouldn't take so long as to be uneffective, but yea, maybe 50 in 1 cage isn't the best of ideas, even if it is still feasible.
5. The animal trainer bond is a loose one, and not a proper pet bond. All it does is make the animal follow the trainer around like a pet does, instead of hanging out at a meeting hall (assuming it isn't in a pasture, cage, or restraint, of course). The trainer gets no bad though if the animal dies. If you put the animal for adoption, or assign it as a war or hunting animal, then the owner will get a bad thought from the death (but also of course be comforted by the pet while it's alive). The trainer bond is actually a handy way to e.g. give your hunter 5 hunting dogs by having him train them, but with no risk of bad thoughts even if they all get killed.
6. In my experience, war/hunting training is pretty quick, gets done within a few days. I've never paid attention to how long the job itself takes. The dog has to be a dog, not a puppy, so at least 1 year old, before you can do it. They won't reach full size until 2 years old, though. Btw, grizzly bears are trainable/full size at 1 and 2 respectively, as well.
Another option is pitting the dogs in, but then you have to make the enclosure bigger, so they won't fight each other to death (1 tile per dog or thereabouts?). You'd still need to trigger a door/hatch/bridge to open the path/LoS, but the advantage of pitting is that multiple "pit animal" jobs can be queued simultaneously.