Drug use is almost always a symptom of a root cause which cannot be identified until the masking is at least under control. However, it is possible to have an alter who is dependent on drugs or alcohol, in which case, I'd say your therapist has been treating or getting through to an alter . . . Nevertheless, the drugs use needs to be minimized at least in order to get to the bottom of everything.

Drugs and/or alcohol are rarely, if ever, the cause of anyone's "issues". 99% of the time, there is an underlying problem that the patient is dealing with in an unhealthy way, even an alter.

Depending on how you've presented for therapy, I'd say your therapist determined that it would be too stressful to the system to mention or try to remove them because it would have caused additional stress, but I promise you if things didn't calm down for you with the drugs at some point, he/she would have addressed it.