@SaiWa Pretty detailed post where you forgot to mention your platform. If I remember correctly, you're on X-box. I know they're having issues, it's a good idea to keep track of what happens, when it happens and what changes / mods / events are affecting the bugs.
As for your questions:
-The horse attacks: Skyrim's wilderness is unforgivable. Even at you manor, nobody is safe from an attack. Horses tend to run toward an attack, even when the attacker outmatches them by far. I know there's a mod for better horses but I never tried it. The best way not to lose a horse is NOT to have a horse in the fist place.
-Issues and bugs: normal when they happen here and there, abnormal if they keep happening at the same place, even in different circumstances. Keep a log like you seem to be doing and browse the Bethesda forum, issues are addressed quickly over there.
-Arrow aiming: broken from day 1. The easy way is to aim lower than your crossair when near, at the crossair in mid-range and over the crossair at long range. It's pretty reliable if you practice intensely at different range. I only use bows against dragons and I only use the Bound Bow, it is reliable and strong. Bound Bow doesn't use "real" arrows but I guess they still make sound if they hit something next to an enemy.
______________
-I know there are issues with the manor management and the Steward system. Normally, you assign the follower to be the Steward from dialogue, not from just letting him/her there. Talk to them, an option will appear if they're not already considered the Steward.
Don't worry too much about Illia, she can take care of herself. I wouldn't leave her there without leveling her up a little bit though. Bring her with you on some of your adventures! She's lethal and she's level capped at 40. She will gain levels fast if you bring her with you in a couple of Draugr tombs. Give her a Circlet and a Robe of Destruction, she will unleash freezing hell on your enemies. Give her a staff of whatever, she will use it while casting with her other hand.
She's my main follower. I gave her a staff of Flame Wall: she spreads Fire with one hand and Ice with the other! She's incredibly resistant to everything it seems: I never seen her die. I'm lvl 50 and I strictly play on Legendary: Illia just never dies. I don't use destruction magic but my battlefield is so full of fire and ice, I can't see what's going on!
She's awesome at slowing an enemy with ice while he crawls across a long fire wall. Few make it out of the fire and if they do, they get the frying pan: Dawnbreaker will break their dawn! I truly love Skyrim!
