It can be an issue, especially if using mild overdrive that doesn't differ that much from your clean sound. Mixing a sound with a delayed copy of itself is a bit like applying an EQ with a bunch of notches like this:
No problem using an LS-2 with analog pedals, just when mixing an analog signal path with a delayed digital signal.
I don't think anyone tries to get comb filtering deliberately when bi-amping... Often that'll be done entirely analog (e.g. DP3-X, or 2 amps) or with both high and lows going through the same digital processor (e.g. a Helix). But even if you put just your highs though a digital pedal, you wouldn''t get much in the way of comb filtering since the 2 signals would be so different that they wouldn't interfere that much with each other.
A different kind of latency. The comb filter effect comes from very short delay times due to the basic analog/digital conversion, which is normally so quick as to be imperceptible. Pitch algorithms have a much larger latency that's very noticeable because they need to slice up and analyse the incoming signal. You'd get comb filtering if you had the dry signal dialled up on the Zoom and then mixed that with analog dry signal via the LS-2 though.