Yeah, it crossed my mind, but it's far from perfect.
It's not only laborious for the user, it wastes server resources and is actively harmful to the host on the long run. If the user has to upload the site and databases twice... well, he'll take twice the space, twice the connection. How could it be better than allow a couple of subdomains CNAMEs for a single site?
If I remember it right 000webhost used to allow subdomains. It makes little sense to keep offering PHP, databases, apache when you cripple those dynamic features by not offering a way to use subdomains in an age when it's all about user friendly urls and SEO.
Hence the suggestion for the devs (this isn't a support request, the thread should remain on the suggestions section). Please, please enable a couple of custom subdomains for each site. Limit it to a fixed number if needed, but let users make full use of the host features. It's not helpful only for the users, it spares server resources.