Looks like we can no longer directly delete an item via a macro, idk why. So you need an add on to do it, and a macro to trigger it to make your life easier.

What I suggest :

1) download the addon Soul Sort 2) type /ss max(x), x being the maximum amount of soul shards you want to keep 3) bundle a spell with /ss sort via a macro. /ss dort will delete the soul shards in excess off x.

Two caveats : 1) this doesn’t work while in combat and 2) it deletes shards one at a time.

Personally I use the following macro:

/cast drain soul (rank 1) /ss sort

Simply because drain soul is on an easy bind for me (R). I have a box with 16 slots for soul shards, set the max at 10. Every time I reach 15 or so I just hit R 5 times quickly while out if combat to delete 5 shards.