As Vampire said, reprisal waves behave like normal waves, but are sized based on the resource cost of the units you've lost in AI territory. Gate-raiding will control where they come from, but as he mentioned, there is also free-floating "Threat", so every system you own should have at least some defenses. If you destroy every AI Warp Gate adjacent to your systems (or lose every system that the AI could Warp to) then waves will appear in AI territory as "Threat", and you'll no longer have any idea where they'll go.
There is also a "secret" wave size modifier based on how many human systems the AI has Warp Gate access to - if you Gate Raid to reduce access down to just one of your systems, the AI will send larger waves than if it could potentially a dozen or more of your systems.
So, yes, it is always worth having at least some defenses on all of your worlds. Your primary defense world, frequently called your 'whipping boy' around here, is where you put the galaxy-cap items like Fortresses or HBCs. This is usually along the path that exowaves take, since those are considered a primary game-ending threat, where waves are normally considered an annoyance.
As for anti-bomber defenses, as he mentioned, Bombers have a Polycrystal hull type, so units with a bonus against Polycrystal will work better against them. Specifically in this case, Sniper, Missile, and Laser turrets have bonuses against Polycrystal. Sniper turrets have infinite range, Missile Turrets have a very large range, and Laser turrets are awesome because they also have a bonus against Heavy ships.
Tractor units are uncommon, yes. The Tractor Turrets (Mk I-IV) are the only turrets with tractor beams. Additionally, there are EtherJets, Spire Tractor Platforms, Riot Starships with the Tractor module, and Black Widow Golems... and Astro Trains, but I think that's it.
If you want other ways to stop AI units from moving, you can look at Gravity sources (Grav Turrets) and Force Fields - most non-mobile Force Fields prevent enemy units from moving through them, which can produce a temporary wall effect. There's also EMP - Warheads and mines can produce a temporary 'stun' effect.
Edit: Just checked, there is a shortcut for "Select all Military units". It's under View Controls, planet controls. Mine is set to Control-comma, which is probably the default. I usually shift-click units on the unit bar to the right.
In case you haven't already, I suggest perusing the
AI War Wiki a bit. Some of the information is a little outdated, but it has things like hull types and bonuses listed for every unit. You can also repeatedly press F1 in game to cycle the unit bar through a library reference mode, which lists the stats of all units in the game.
Finally, I think you may have read it already, but I'll mention it again: read the
Excellent Guide by forum member Kahuna, to get some good tips on how to build your defenses.