That depends. If you build a custom mattress that's both within the regular depth range and in the standard size run, you should have no problem finding sheets for it just about anywhere.
If your custom mattress comes in a non-standard size, things can start getting dicey. Most of the time, you will be able to get sheets for European mattress sizes or common non-standard sizes (think Alaskan king or Olympic queen). Sheets for these mattresses might be a little tougher to find, but they're out there.
If, however, you get a mattress with a custom shape – especially one that's very far from the standard rectangle/square – you're probably going to have to have custom sheets made for it as well.