There's all kinds of rumours as to how Apple pics its store locations out there, but I think it's fair to say that they are very picky as to where they set up.
In reality though, no one but Apple knows why no store here. I've heard that it was considered, but the "prime" spot would be Grafton Street (they live the so-called fancier shopping districts and also like it when there's a university nearby). While they should be able to negotiate a decent rent, when sighting shops in streets rather than shopping centres, they do like to make the building distinct. If I had my guess (along with numbers probably confirming the Belfast store and CompuB service the Irish Market well enough), it's the renovations they'd want to do on the building that would be an issue with planning and that they aren't affraid to wait for the right spot to become available rather than taking the first available empty store.