They won't.
They won't touch anything after Enterprise.
I'd actually wager a $2 rare against you that something might show up from starfleet academy.
But then I would also bet it would be more in the commander set than in the regular expansion.
Here's my logic:
By my estimation, they would have been working on the set when SFA was in development. See the wiki says the show got an official series order in 2023. MTG averages around 2 years in development. So if they MTG started on the ST set in 2024, that would be right as SFA is being filmed. ST set is being released in Dec of this year, right in the midst of Academy's second season. Given the way corporations, markets, etc works, that's where my bet is coming from. WOTC and Paramount would have absolutely been convinced Academy was going to be a big hit, revitalize the brand, and so as it hits its second season (to thunderous applause), the MTG cards would hit store shelves, and they would have perfect brand synergy, leading to both selling out.
At least that was their hope. And given the lead times you need to make and distribute stuff, (the cards should just about be made or getting prepared to right now as we speak) if there was anything Academy related in the Trek set, they would have no time now to try and remove it. (At least not without eating a big financial hit.)
But then I'm old enough to remember the old promotional material for Voyager where they called the doctor on the ship. "Dr. Zimmerman" and the predictions that Neelix would be the breakout star of the series. (Heck I think I still have those TV guides.) So it is my experience that things can be out the door and filled with bad predictions. Academy may not get its entire cast into card forms, but they would possibly do some cards of the "predicted" breakout stars.
Heck I wonder if they're going to do just the one commander deck like Turtles, or are they going to do "era" commander decks like Dr. Who? If the latter I could see then a TOS era, TNG era, and then a Kurtzman Trek era. (Hm, who would be deck #4? Kelvin timeline era?)