If you think Arcana and History are bad, wait till you only get Nature checks up to Myconid colony and then they never matter again. Or animal handling when 3 classes in the game can cast a trivial ritual speak with animals. Or survival, the worst of them, with occasional hidden chests to dig up that don't have much and even then if you fail the roll you can still dig them up.
A LOT of checks besides just persuasion/intimidation/deception/wisdom just stop happening in any meaningful sense after Act 1.
Yeah, being able to just dig up chests by using the shovel when you see the failed roll was a funny discovery. At least this can be easily fixed by hiding failed rolls.
The overall lack of Intelligence checks, especially meaningful ones, is just what we’d call bad DMing if this were a tabletop campaign. I just hope there is still time to fix it without having to record hundreds of new lines of dialogue.