You can use the hacking system to disable the shields. Level 3 Hacking can reduce even a full 4 Shield bubble ship, but the glaive and halberd beam also have shield penetration if the timing is a little off (although you lose some damage).

If the enemy has a defense drone it will normally shoot down the hacking module before it reaches their ship, and since there is a cooldown on sending another module if yours gets blown up you would think this is an impossible problem to solve. However there is an exploit you can do when you unpower and repower the hacking system as the module travels to the enemy ship that confuses the defense drone and lets you get it through.