What can Blood Stone Shards be used for?
Solution 1:
Blood Stone Shards are only used for upgrading weapons up to +3. You need 3 for +1, 5 for +2 and 8 for +3. That means you need a total of 16 shards per weapon to get to the next upgrade material tier.
The further you advance in the game, the more Blood Stone Shards you will come across. The same goes for the Blood Stone of higher tier (Twin Shards and Chunks). If you have an excess of materials, you can use them to upgrade weapons you don't use so often or sell it to the messengers in the Hunter's Dream for 200 blood echoes each.
If you try to upgrade all weapons you come across, you shouldn't have too many left though. I recently had reached my inventory limit for shards and still didn't have enough to upgrade all my weapons. There is no other use for Blood Stone materials that I know of.
Solution 2:
It sounds to me like you only have a couple of weapons that you use.
If you only have a couple of weapons, and they're fully fortified until the point where you need Twin Blood Stone Shards; then use the money to buy the other weapons.
Some of them are useful for different things, e.g. the Cleaver. Other weapons like your firearm and torch can be fortified too.
If you haven't got much spare money yet, don't worry you will have soon enough.
Either that or the total opposite extreme is true, and you've bought all of the different weapons, and fortified all of them; after replaying a lot of the levels over and amassing a lot of Blood Stone Shards.