PokerStars - $0.05 NL FAST (6 max) - Holdem - 6 players
Hand converted by PokerTracker 4

BTN: 100 BB (VPIP: 27.18, PFR: 23.30, 3Bet Preflop: 5.56, Hands: 106)
SB: 120 BB (VPIP: 20.83, PFR: 15.28, 3Bet Preflop: 3.85, Hands: 72)
BB: 130.4 BB (VPIP: -, PFR: -, 3Bet Preflop: -, Hands: 1)
Hero (UTG): 112.8 BB
MP: 107 BB (VPIP: 25.93, PFR: 22.22, 3Bet Preflop: 12.82, Hands: 82)
CO: 66.4 BB (VPIP: 0.00, PFR: 0.00, 3Bet Preflop: 0.00, Hands: 4)

SB posts SB 0.4 BB, BB posts BB 1 BB

Pre Flop: (pot: 1.4 BB) Hero has A Q

Hero raises to 3 BB, fold, fold, fold, SB raises to 10 BB, fold, Hero calls 7 BB

Flop: (21 BB, 2 players) 6 6 6
SB checks, Hero checks

Turn: (21 BB, 2 players) Q
SB bets 13.6 BB, Hero calls 13.6 BB

River: (48.2 BB, 2 players) 4
SB bets 30.4 BB, Hero raises to 89.2 BB and is all-in, SB calls 58.8 BB,

So I think one of my leaks is that I raise or bet with hands that have middling strengths, making worse hands fold and better hands call.
In this hand, I think my river raise is good, because all flushes will call.
However, if the river is 4 of another suit, is my river raise ok? Hands like pocket pairs less than Q won't call because I'm repping a Q, and KK,AA,6X will call.

just call

Fold pre.
AP just call. What worse hands call you? You either split or lose a big pot

I think it's fairly close, as you're near the top of your range, but villain can definitely play AA, KK, QQ and a random 6 like this, so you should just call.
He shouldn't really have any worse boats that can call a shove, because it would be weird for him to check the flop with JJ/TT/99 and then bet the queen turn.

thats a really bad river shove

Just call, only chops or KK/AA call a shove.

Fundamental logic and handreading issues going on here.

Never in a million years is he calling river with a flush, fold pre, can 4b sometimes too, not flatting

Call, fold pre

I'm quite surprised at the amount of people folding pre here. Call river.

In a normal game it's a bad shove, in a raked game it's a disaster, the worst hand he will call you with make you lose money anyway.

It's not terrible to slightly overfold pre in this spot, imo.

The river on the other hand is pretty bad, in particular OP's reasoning, like Roger Floperer pointed out above. It's not short deck where a flush beats a FH.

I read somewhere that AQo facing a 3-bet preflop is a call IP and a 4-bet bluff OOP (against standard reg), but the article is probably not about microstakes.
For the river raise, is it because only AcKc will call my raise and lose? Because if I had AcKc I would have called the raise. So my raise is only good against this single holding.

that's a serious leak lol

Facing a 3b from a tight player after you've raised UTG, where your range is strongest, means the V 3b from the small blind likely has an absurdly narrow range. It's probably a BE to slightly losing call with AQo against this particular V. AQs can easily call.

As far as your hand reading goes, it needs some work. With this flop, any pair held by either player makes a FH which beats a flush. V should not value bet river, nor should he call a river shove, with any flush on this runout. If you would call a river shove with a flush, it would quite literally be lighting money on fire.