I know none of these are particularly damaging, but figured worth cleaning up either way.

Inside of data/pixelmon/config/shopitems.json,

Using old style item references which prevents a player selling balls to the shopkeeper.
Every entry from pixelmon:poke_ball to pixelmon:safari_ball should be converted to their NBT variants.
Note: by extension the current NPC shopkeepers are also to be updated as they use the old names, will now need IDs for the NBT variants.

Inside of data/pixelmon/drops/pokechestdrops.json,

Neither are pokeballs but have been edited with the Pokeball NBT:
pixelmon:light_ball
pixelmon:smoke_ball

Inside of data/pixelmon/drops/pokedrops.json,

Using old style item references for ball/lid on the following Pokemon:
Voltorb
Electrode
Snubbull
Granbull

Inside of data/pixelmon/loot_tables/special/common_pokestop.json,

One ball appears to not be converted to the NBT format whilst others are:
pixelmon:ancient_great_ball

Inside of data/pixelmon/loot_tables/special/rare_pokestop.json,

One ball appears to not be converted to the NBT format whilst others are:
pixelmon:ancient_ultra_ball

Greetings,

Confirmed and forwarded.

Thanks for the excellent work/descriptions!