DoctorGOGgles: The bombs may be in one of the quick use slots (top right of the inventory screen or cycle through them with the 4 key). Bombs, traps etc. that are in one of those slots don't show up in the normal inventory.
Good thought, but not in my case. I used everything I had against the first endrega queen, bombs, knives, traps, and then tried to make more the get the second one.
Anyhow... that was pre-patch. I've not bothered with them after.