Yep, technically that's how it works... but it should be noted the rules aren't expecting you to have 100 Mooks in play at a time.
There's no limit in the write-up, but there's probably a common-sense limitation that's implied by the narrative. What constitutes one "fight"? If a PC took this to the Paris WWII pop-up juncture, the character probably wouldn't expect to be able to stop the advance of all million nazis on the entire Western Front with just by firing his pistol at one squad.
How to reign it in, and indeed whether or not to reign it in, probably depends on how often you expect 100-mook fights to come up in your game. If this is the final battle of a long campaign / the culmination of a major storyline, then I might be inclined to just let it happen. It's crazy, but it might be just crazy enough to be a big memorable moment where this one PC saved the day. Maybe let 'em have their glory?
On the other hand, if 100-mook battles is something you expect to be a mainstay of your campaign, with at a half-dozen such fights over the next few months of play... then it's probably a good idea to figure out some way to limit it the schtick so it doesn't render mooks entirely useless and undermine the willing suspension of disbelief at the same time. I mean, hordes of mooks are a classic trope of the genre, and you'd probably hate to see that edited out entirely by a single schtick in an un-fun way.
A few ideas on how you might limit it, if you're so inclined:
Sometimes split your fights up into multiple sub-locations or sub-fights, and tell the player that ability only affects the mooks on one of the smaller battlefields. "You can either shoot out the front door, or out the back window. Do you want to suppress the ones out front, or the ones out back?"
You could split your mooks up into hierarchies, and say it's about chain of command. There's 30 Yakuza hitmen, 50 wasteland ruin runners, and 20 mook cybermonkeys. Every time you activate this, it effects the group that corresponds to the target you shot. The other two groups aren't affected, because their commanders are forcing them forward if they aren't the ones being shot at in this moment of the battle.
Put some other mechanical limitation on it, and explain to the player that the power was written with the assumption a typical session wouldn't have hundreds of mooks... "for a campaign as epic as ours, it needs to be tweaked". A possible/reasonable limit might be: on a successful hit, it suppresses a number of mooks equal to the Action Value + Swerve of the attack. You rolled an 18? Cool, you kill 1 mook and send 18 others diving for cover.
Sometimes give a Featured Foe a special Foe Schtick that lets him spend his actions to cancel it, or otherwise boost the Initiative of his mooks. They're losing out on 100 mooks suppressed, but compensating by forcing a Featured Foe to do nothing else for the entire fight to keep his men effective. If you go this route, every once in a while make sure you don't give any GMCs such powers, so the character gets his badass moment. Probably start with your first fight being one where there's nothing like that, so the player knows up front that they'll get to bring the awesome at sometimes and aren't always being nerfed by the perfect NPC build to counter them.
House-rule that the mooks only have to spend 1 shot per activation, instead of 2. Most turns the mooks will still get to take a shot or two later in the sequence (at least until another PCs decides to double-up on this schtick), but you'll definitely still delay them and buy time for the group to thin them out a bit before the mooks get to attack.
In general, I would try to avoid situations that are likely to make the player feel like he or she is being punished for taking the schtick, or would have been better off if they'd never taken it. Saying "It can't affect more than 20 mooks per attack" is probably a better limitation than "all the Featured Foes and Bosses only attack the PC who has the schtick, in every single fight of the entire campaign".
A better version might be something like "when you use this, you can decide how many mooks it suppresses, but for every 20 affected by it, one more Featured Foe will decide to target you exclusively." That way the player can use just a pinch of it for flavor, or decide to make a big sacrifice.