It will absolutely come up. And people will remember it. It will absolutely be perceived as "cheap ass founder didn't want to pay worker for their time."
However paying them will be remembered too. It will be perceived as "why are you giving away profitability of the company (and thus my equity and/or end of year bonus) to someone you should have fired a long time ago?".
The answer to that is “they worked 50 out of the 52 weeks; it was a leadership mistake earlier to not hold everyone to the high bar we expect, but we still act ethically towards all of our stakeholders, even when doing so is inconvenient.”
Yeah, sounds best. I'd still run it past the lawyers to make sure it's fine to "badmouth" a former employee in your jurisdiction.
It means taking ownership of the mistake, even if it does mean that you're effectively apologizing for devaluing the company to the other stockholders and other stakeholders.
Still, there's a little bit of "oh, so when I leave I can expect management to talk shit about my performance", which wouldn't do wonders for my impostor syndrome.
