1. Assign suitable ones as scholars (not scribes: those are just copy machines), provide tables, chairs and quires (or other forms of writing material) in the library. However, visiting scholars tend to be more productive.
2. Don't. It's broken, as your fortress will eventually crash due to the equipment corruption bug. Sure, you can get a dozen, or maybe even a score of years in before it happens, but eventually it will happen (I stopped playing after having lost my 5:th or so fortress due to this bug).
3. Don't think there's any really good investigation made. It seems a full squad can often take sites with about 100 inhabitants, but note that trolls/ogres/blizzard men (goblins), or elephants etc. (in the case of elves) are not included in the number of inhabitants.
4. The most likely cause is a hole in the roof somewhere resulting from cutting a tree. Snatchers sneak, so if your guard dogs are poorly placed and you have no traps they could possibly get past those.
There's also a bug (mostly squashed, but cases have still been encountered) where the whole fortress goes into chaos where inhabitants and visitors start fighting when a siege happens. I've never seen an actual spy, but goblin civ members come as members of performance troupes and report the location of the traps they've seen back to their civs (in fact, all visitors do that). However, I haven't had that kind of spy inside the fortress at the time of a siege, but I wouldn't be surprised if they'd align with their civ.
5. It's been noticed, but not explained...
6. Temple dances are exceedingly rare, so don't bother about that. Also, I'd focus on socialization in the tavern rather then the temple(s). I've never overlapped the social zones (science basically happened after I stopped playing).
7. Mood management through crafting will likely have to be overseer management intensive, or you'll have some non crafter(s) hogging the "hobby" workshop excluding the others and neglecting their real duties. There's no good answer for that one.
Militia rotation doesn't work properly as off duty dorfs spend almost all of their time on individual training rather than their civilian job/R&R. However, someone recently came up with the clever trick of burrowing everyone (civilian alert burrow) in a burrow that covers everything except the training facilities. That causes them not to go there except when on duty (and a bit of burrow management when you need "real" burrows active).
Siege cleanup is a serious danger to fortresses currently.
The best usage for mine carts is as part of (mine cart) quantum stockpiles. If your fortress has permanent activities far apart from each others it's possible to set up mine cart routes to carry materials between them, but it's a fair bit of work, and you need to block access to critters from automated paths or get a self reinforcing roadkill explosion eventually. Barrels (such as booze) and bins cannot be transported with mine carts (they're manually hauled back to the feeder stockpiles due to what's presumed to be a bug).