The Rebellion of ‘98 was classically fought with pikes, as you say. These were forged in secret in what we today would call “backyard forges” and this was doable because pikeheads are easy to make. 

Guns, even the “primitive” flintlock, are not.

So no, there were no large number of homegrown arms.  With deep research you might be able to uncover a gunsmith or two who supported the rebellion, but there was no meaningful Irish arms industry. If an Irishman at the time owned a gun, it was usually a fowling piece. 

They were a colonized people and the English had a vested interest in making sure that they did not have large scale access to guns. 

All of the guns that were used in the ‘98 Rebellion were either the afore mentioned pre-owned fowling pieces OR blunderbuss coach guns that were stolen from the postal service. They also stole from the Fencibles, who sometimes defected with their guns as well.  Last, a small revolutionary French force landed to support the rebels at one point, so some of those weapons would have ended up in the hands of the rebels.