Just give them moderate status effects.
Deadly Crystal bomb (elemental): Poison
Deadly Splinter Bomb (piercing): Shock
Dark Matter Bomb (shadow): Fire
Deadly Shard Bomb (normal): Freeze
------------------------------
The above would at least put them all on par with one another, though it might be necessary to buff dark matter/salt bomb a bit more than the others- dark retribution is just so much better as a DPS option. I'd possibly do the following-
Salt Bomb: Change slime buff to low, deals both fire and shock; each crystal either deals fire or shock, never both.
Dark Matter Bomb: Curse
A curse variant would probably come across as OP due to how players over-value the status, but this might not be a bad thing. The actual curse status would quite often fail to help out in a meaningful way, though in addition to the shard damage would give it a meaningful advantage over dark retribution.. which would still outperform it in terms of raw damage.
The normal variant of the bomb has truly despicable damage and may also want to receive a disproportionately awesome buff. Perhaps it could be given all 5 of the 'big statuses' in the same manner salt bomb could have fire and shock- where each crystal is randomized.
------------------------------
And seriously, fix the invincibility frames bug. If it weren't for that the piercing shards would be able to fight enemies like greivers, and so would be top tier just like dark briar barrage... imagine hitting a charging griever with a shard, just to have the griever go 'tink' and crush you anyway. Go in game and try to fight them- it's doable up until the invincibility frames get you.
Gremlins have low affinity for fire damage and beasts take minimal shock damage.
The 3 flaws the bombs have are simply a matter of numbers. The payload takes too long to release, it's too weak and is crippled by the hit limit - something that defeats the entire purpose of having shards in the first place.
We all know they will never get fixed. The fact of the matter is, if you really want to shard bomb, don't use bombs at all - use the Tortoguns. It shouldn't be a problem, because it's not like you're going to use Mad Bomber, right?