I did at first. With 20 years of sporting clays, FITASC and stockmaking under my belt, my preferences (including flat shooting) were firmly ingrained. Also, from that background I knew that bead-checking spelled miss. But I knew enough to know I didn't know anything about trap except that higher shooting guns predominate. So I started with an open mind and a secondhand BT99 with 2 beads and an adjustable comb; the first I'd ever owned. After a year or so and a few thousand rounds the settings were right.
So I bought a Perazzi TM1 from Smokin Joe, restocked it with English walnut to fit me, without adjustments, and started shooting. I still checked bead alignment but MADE VERY SURE that my focus was beyond the trap house before calling. Watch any shooter who mounts the gun, wiggles and squiggles, stops moving for a millisecond and calls...then bet against them. For sure, sooner or later, they will be surprised by a target.
I removed the center bead and virtually never bring the front bead into focus. I don't even look at my gun. Once the gun fits with the perfect amount of cast the center bead has served its purpose and is now useless clutter to me. Worse than useless since, being even closer to the eye, it's tougher to ignore. Of course I "see" the muzzle and bead when approaching the target. But I start by keeping my focus some distance out in front of the trap house and don't allow myself to ever focus on the roof, not even for an instant. For 10 seconds the most vital thing in the world is to SEE THE TARGET. If I can see it, I can kill it. After the shot, I go back to looking for 4-leaf clovers. Of course, it happens on rare occasions....my focus goes to the wrong place...and when it does I do a total reset. Drop the gun, focus out, mount, settle and call.
If you can focus on the beads, wiggle and squiggle and then ALWAYS shift your focus before calling, by all means do it. Knowing your mount is correct is hugely important to your confidence. And confidence is a huge factor in shooting well. But having to check beads is a potential pitfall that can be eliminated altogether with a gun that fits.