Should we say "they are high enough as they are" or "they are high enough as it is."?

Yes, that would be perfectly fine. The two phrasings mean basically the same thing, but with a difference in what you’re talking about.

When you say as it is, the subject it is a generic ‘it’ that refers vaguely to ‘the current situation’ or something like that. It could be rephrased to “the way things currently stand” or “in the current state of things”.

When you say as they are, the subject they refers back to the taxes and is therefore non-generic: it has a specific, concrete antecedent in the previous clause. It could be rephrased to “at the level they are currently at” or “in the state they are currently in”.

While it is theoretically possible to make this same distinction with a singular antecedent as well, there is no real way to carry out the distinction in practice, since you’d end up with it both with the generic, antecedent-less pronoun and with the specific antecedented one:

I hope the income tax won’t be increased; it’s high enough as it is.

If the antecedent is a different pronoun, it becomes possible to distinguish again:

I hope he doesn’t win—he’s big-headed enough as [he/it] is!

But in the end, the difference between the two is negligible enough that I doubt anyone would ever bat an eye or even notice in any context regardless of which option you use.