Hot Topic stores sell to the punk group of today. You can call these kids punk, alternative, or whatever you want but the punks of today is who this store appeals to. Of course, Hot Topic wants to keep the sales of this group high. If they fail to do so Hot Topic will go under completely.
Pop punk sales is basically the niche that is Hot Topic. Even if the pop punk genre begins to shrink and the fad dwindles away, there will still be enough of them around to keep Hot Topic up and running for years to come. Maybe it'll eventually fail, but keep cashing in now.
Hot Topic stores keep pop punk sales high because they cater to an certian age group, teen to young adult, that is into pop punk items. Of course they have to keep the sales high inorder to stay in business and continue to provide the items that contribute to the pop punk culture found in this age group.
I would think that Hot Topic would want to keep pop punk sales high since they are making a lot of money off of the people who desire that goth and punk look. If the sales go down then that could end up hurting their business because no one would be interested anymore.
Right now, Hot Topic is endangered because the fad of commercialized pop punk has gone down the gutter, but it's the perfect time for them to capture a second zeitgeist, like the commercialized "fake indie" that has become more prevalent with teenagers, or perhaps popularizing the increasingly (thankfully) marginalized screamo movement. Either way, it's up to Hot Topic to follow trends, not push them.