I suspect this will have little affect on airport service.
In terms of frequency, the Saturday airport schedule is virtually identical to the weekday airport schedule.
In terms of crowding, most of the airport runs I've been on have been less than half full, so I highly doubt anyone is not going to get a seat.
The most affect I can see is whether the trains are affected by spillover delays from other lines, i.e. some airport line trains originate in Glenside, Warminster etc and could be delayed on their inbound run to Center City. But on a line with service every 30 minutes, it's hard to see delays being too terrible.
If you want to connect to another SEPTA line, or Amtrak, at 30th Street Station of course, that's potentially a different story.