Subsystem targeting gives a chance for system to go offline. The standard effect is that it drains power, making energy weapons deal less damage, shields regenerating more slowly, ships moving slower and science abilities being less effective (on the enemy). You may get lucky and get an offline system, but the drain is useful too. Not on PvP but on PvE. I like watching my enemy NPC's weapons get nerfed...
IIRC they changed this sometime last year so that only the Level III version of the ability would take subsystems offline.
[6/24 23:12] [Combat (Self)] Your Thalaron Pulse deals 126254 (48978) Radiation Damage to Tactical Cube. Hehe. Suck it Borg!
[10/8 15:47] [Combat (Self)] Crystalline Entity deals 98082 (147136) Kinetic Damage to you with Warp Core Breach. WUT? I blame Kurland for this and all other problems in STO.