i'm talking specifically on boards that have a lot of cards in proximity to your own but nothing really connects to a degree that matters

take Q9o, beats atc 55% of the time

an 86J flop feels good here, so in a hu match you're ok with this flop

yet your equity vs atc just dropped to 49%

meanwhile, swap out that J for an ace, and suddenly the 86A board doesn't look so hot and yet your equity vs atc has barely changed to 46% - which is the same as 587 board, another one that looks pretty nice for Q9o

Do other players suffer from this too of having to remind yourself not to get tricked by deceptively looking flops? If so why?

I'm not even talking about blockers or any other of the more meta reasons why you could argue (i think quite reasonably) that these are better flops than a pure hot/cold calculation would indicate. The reason being I'd always felt this way about flops like this since high school when i didn't know anything and thought hands like K4o were good to raise with preflop cause it had a king in it and never even considered position etc etc.

Is it a mental trick or do we recognize some of those higher level things on a subconcious level and just aren't able to verbalize it other than our brain saying "I like this flop"?

Equity against ATC isn't that important IMO. Poker can be viewed in a much more profitable light by thinking "ok, I think my opponent will fold most of the time if I bet this amount; I think my opponent will call most of the time if I bet this amount; I think my opponent will check/bet most of the time when I check here", all considering what your opponents range is, what he perceives your range is. and blah blah blah.

But generally, bet.