Y adapters are fine to use, and their function doesn't indicate any engineering deficiencies. All it does is increase the input sensitivity, and the only tangible result is you'll need to turn the gain down on the subwoofer because it's a bit louder. For a subwoofer that is reluctant to come out of standby mode the use of a Y adapter is often the only viable solution.
In your case, however, it seems you have the opposite problem. The link above pertaining to ground loop issues would be a good place to start, because the hum you're experiencing may very well be that. If so, that could be why it's not going into standby.