Are Great Knight Medals in any event shops?

Nero fest, you can farm as much as you want in the lottery box.

Summer Mordred needs 16 and Arturia needs 30

The Chaldea Summer Memories shop coming out next week (~2weeks) has 20 Medals total

Nero Fest coming out in the Autumn has 3 medals per lottery which will take quite a decent amount of apples if you want a decent amount of them.

My best advice is to farm Sovereign Castle (Camelot) during event downtimes so you don't end up hard farming the lottery or event nodes for the last remaining medals you'll need