Comics without covers are hidden when browsing, but they show up when searching (entering things in the search bar). I believe this was done so that newer users to the site could be presented with an appealing browse page, while still addressing the concerns of those who are looking for older comics, just not as well as the old banners do. You can view the banners for comics without covers in their profile, so you can find these old comics, it's just less convenient.
There isn't really a tidy way to use banners for those comics that have them but not covers in the search results, which is probably why it hasn't been done. I'd rather the search results be designed for the future where coverless comics grow less relevant, but it does suck in the present when a majority of comics lack covers because they're old.
That said, a lot of the older comics without covers uploaded actually do have covers, often their first page or so. A lot of these even use the same art as their banners. It would be nice if comics without covers had their first page displayed (perhaps slightly greyed out to indicate that it's automatic), or better yet, if the first page of a comic labelled a "cover" could be assigned as the cover. After all, if their authors ever come back, they can just change the cover to something better if they want, and if they don't come back, then at least their comics will be in a better place than having no cover at all.