How long will side-quests last for

1. You can be detected by these people and still get the reward for being sneaky. As long as they don't go Hostile, you're fine.

2. You can make this jump without the leg aug, but you need the Punch Through Walls aug to go this way. This also involves snapping a guy's neck and will ruin a pacifist playthrough. Also throwing a grenade at the wall works, and only knocks the guy unconscious., or you could just use the ventilation ducts attached to the wall...

3. As before, if they don't go Hostile, you are fine.

The game will tell you if you fail the sneaky objective.

The combat rifle is probably the easiest to get to. Almost every soldier, even at the start, will carry one.

A revolver is also carried by some soldiers, but less frequently, so I would put that on number two. It still won't take too long into the game though.

The first I've seen a stun gun was also somewhere in the early game, when I started for pacifist.

Seeing as I've had a tranquillizer rifle from the start, I've never bothered to look for one, but they are also present quite a bit in the first few missions.

To sum up, I don't think you'll have to wait long for any of the weapons, but the ones for up close are going to take a bit longer than the ones with distance.