Ion Modulators will boost energy based weapon's damage per second against shields increasing its shield draining potential, but suffers a decrease in firepower against armor.
The use of ion modulator has good potential, generally mid level players rely of heavy shielding on their ships such as Shockwave IV or Spectral V shields to protect their ships, the prevalence of high level shields may incite players to invest in this weapon booster to increase their ability fighting against shielded targets.
They are not used as frequently amongst high level players, as high level ships often have massive amounts of armor. So much armor so that the armor damage reduction penalty is enough high enough to outweigh the advantages of higher shield damage. That is, if you equip ion modulator, your ships will take longer to destroy enemy ships because of the armor damage reduction and the high amount of armor on enemy ships. This is only in high level ships, particularly Iron Star Company hulls.