Is it bad to use a rotary phone in a logo? Well, no if you are a phone company. But probably yes if you are a cell phone store.
Is it bad to use a turntable in a logo? Well, no if you are a vintage record shop. But probably yes if you sell modern audio equipment.
So, is it bad to use a pointer in a logo? Well, no if you sell mice/pointers. But probably yes if you just use the web as a sales outlet.
For e-commerce, it's difficult to say if a mouse pointer is outdated. There's a fine line between being immediately recognizable and cliché.
As of 2013 more people access the web via mobile devices, so yes the pointer notion is a bit dated. But, as an online company some of the more cliché images offer immediate recognition - globe, pointer, etc. So it's easy to fall back on those. It doesn't make them inherently "bad". It is the overall usage that may be a bit trite or played out.
Look at alternatives for e-commerce on mobile devices... a finger? a cell phone? These clearly don't convey the same message that a pointer does, but they would be more accurate.
I would ask is any indication of the web even necessary??
Look at brick and mortar stores (Target, Wal-Mart, Sears). Do they all include a building in their logo? Of course not. But that's the primary place you go to buy. They don't focus their logo on the sales outlet they focus the logo on the company. And I think that is the primary difference with e-commerce. E-commerce sites are often less experienced and more quickly constructed so less time is taken with what, we as designers may see, as the more important aspects of branding.
A logo should most often reflect the company and possibly a philosophy, not the location. By using a pointer or any "online" indicator the creative possibilities are greatly limited. You tunnel the company into an "online-only" perception and viewers think of the "web" first, then the company second. That is generally not the goal of a logo.
If the online-only store sells, oh, herbal supplements, I'd focus the logo on herbal supplements. Or if it's an online-only pet food company, I'd focus on pet food/supplies for the logo. I would not focus on the fact that it's an online store only.
In the end, it's not inherently bad to use a pointer... it's just a bit lazy.