Then again, that entire Cube was badly hurt by what supposedly were 8472 starships; the Drones could have gone down as part of the Cube, rather than as victims of personal violence.
On the matter of using bullet guns as an alternative when phasers fail, I'd argue that phasers are inherently more reconfigurable than bullet guns. Thus, it might be more worthwhile to try and find new modulations on your phaser than to go and fetch a bullet gun that will only work once and can never be modified or modulated.
On the matter of the Drones moving slowly and not engaging in counterattacks or fancy martial arts moves... Perhaps the Collective deems it more valuable that they continue their original work, or fight the intruders by operating the Cube rather than by combating the boarding party directly? Difficult to find a good justification.