Here is my favorite late game Golden Apple farming location. 

The forest in front of the Everlasting Tangle. 

The monsters are those Jooba A, B, C. You can steal Golden Apple from all of them. They come in groups of two or three.

So, with Laka and Ami with mimic stick, you can steal two Golden apple per fight. Three if you want but it'll be slow.

I used Laka and Ami steal then dispatch them quickly with Vera's Bahamut and Oalstan's Apocalypse in one turn before enemies can act.

50 Golden Apples in less than half an hour. Some other shards like power or speed also drop but not a lot.

42 in 10 minutes after I adjust MP regen equipment to reduce time using ethers. lol

I mean its better than buying the apples and shards alone...plus it's all stats+1; why would you NOT farm this lol.  OP!

If you do the marks first you get economizer from one of the elite marks which reduces mp costs by 80% helps with farming a lot, one of the bosses also has a eidolon dress you can steal for vera, which reduces mp costs by 40% iirc.

Overall this is a good farming location, but like you said is slow, sadly there is no easy way to farm a bunch of shards fast and call it a day, thanks to shards and golden apples being so expensive to buy.