I was trying to play along to a song today and anyway this question just jumped into my head.

How do most guitarists count while playing with their band?

Or is it just so much practice its an instinct?
It depends, on some songs I count, and on others I don't.
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As a drummer, who is the main man responsible for counting, it reallt just becomes natural, for certain time signatures. I never lose my self when it comes to 4/4, 6/8 and generic signatures like that, but like most musicians, it becomes very difficult when you start messing around with weird signatures like 7/8, 5/4 and ones of that nature. best way to get good is to jam with someone or something that is on time, like a drummer or to your favorite song, whatever you feel.
I couldn't agree more with arnolddrummer. I am a guitarist but have been a musician for my whole life. I never count with simple time sigs, but yes, when they get complex, like 7/8, 5/8, I do actually count. Sometimes it does help to count outloud and not in your head. Helps get the point across or something
I don't count. I've played enough where I can feel the groove in any time signature.
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i don't. i just look at the music and play it.

if i don't have music, it's even easier -- i hear it and i play it.
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You count until it's second nature.
People say they dont count simple time signatures because they're so accustomed to them already.

Though when I'm playing jazz, I'll still mouth the triplets to myself "doo-uh-la"
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practice by counting along with songs.... eventually it'll be second nature.

also just listen to the music your playing, specifically the other instruments and you will be able to pick up the cues to know where you should be playing.
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I usually don't have to count.

But sometimes there's an aspect that trips me up, in which case I'll retreat into counting until I'll locked it down.
A lot of the odd time signatures are grouped in a specific pattern.
For example 5/8 is often divided into 2 and 3, or 3 and 2.
7/8 might be 2,2,3 or 3,2,2.
This makes it easier to count.
If you're playing in an orchestra the division of the bar will be written in the music and you just follow the conductor.
If you're jamming it or listening to a piece - try to hear the accents of the beats and figure out what the division is.

A lot of the time it just comes down do familiarity and with the overall feel of the music so you end up not counting it at all.