While some of the points in the OP have merit, most do not. Let's go through them one by one:
1) Often you just don't want some cards, neither in your hand (they are useless), nor in you discard (they get shuffled back in the deck when you are healed and you are stuck with them).
This is a legitimate concern. However, it's incredibly minor. How often will this make the difference between failure and success? Almost never.
2) Sometimes there are penalties for failed checks (is some locations, and with some scenario rules), and if you have no chance to acquire anything you could just skip the check to avoid this penalty.
According to the rulebook of the newest set, Wrath of the Righteous, "If you choose not to acquire a boon, it counts as failing to acquire it." So this point is totally illegitimate. Hawk and da-Mayor believe that the Glassworks is an exception to this, drawing a distinction between "failing to acquire a boon" and "failing a check to acquire a boon," but I completely (but respectfully! ) disagree. I think that "failing to acquire" is just a shortened form of "failing a check to acquire" because really, when are you ever going to fail to acquire a boon in any other way? It's possible I'm wrong, but only if the designers simply come out and say it; the rules in this intance are far from unequivocal.
In any case, however matters are settled in the Glassworks, this point is wrong.
3) Beginning with adventure 3 if you don't acquire a boon with BASIC trait you could remove it from the game. Sometimes we chose to refuse a check just to remove a card from the game, so that there would be more new powerful cards in the deck, even though this boon could be useful in a particular situation.
This is also completely wrong. The digital game handles box culling in a different way than the physical game does. In the digital game, whether a boon gets banished has no bearing on whether it will appear in later scenarios.
This is a controversial topic: some players, like me, think Obsidian's method is superior to the physical game's, while others hotly disagree. Either way, though, the ability to pass on boons won't affect what it's in your box in the digital game.
4) Sometimes you banish certain cards on purpose - so that you can choose a card you need from the vault between scenarios. But if you later come by a card of that type in a location you are forced to pass a check to acquire it, which sucks.
This is the only point in the OP that's both legitimate AND significant. At the end of the day, though, it's not game-breaking, so I don't think that on its own it confers high-priority status to the option to auto-fail boon checks.