My question is essentially in the title: is there a well-developped theory of algebraic pointless topology, that is algebraic topology on locales ?
If not, would it make sense, i.e. would it be relevant (for instance the usual fundamental group construction makes no sense for spaces like the spectrum of a ring, because such spaces are usually totally disconnected or at least, really not connected; so one may wonder -if one does not know much about locales, as I do- whether it would be relevant to study algebraic topology on locales) ?
Added later : In particular (although more general information is also welcome, as in Hurkyl's answer) I would specifically like to know if there is a way of making sense of a "fundamental groupoid" of a locale (which would be defined differently from usual spaces, otherwise pointless locales would have an empty fundamental groupoid) that would be interesting ?
One way to answer the question is the observation that sheaves are defined on locales (or more generally, sites or localic groupoids) rather than on topological spaces, so anything that can be expressed in terms of sheaf theory can be interpreted as "algebraic topology on locales".
A category of sheaves of sets is a Grothendieck topos. You can do a lot of algebraic topology in topos theory — as a simple example, you can define sheaf cohomology. This is one of the main lines of development in algebraic geometry.
Regarding the specific interest in the fundamental groupoid, I don't know anything but found these links that may be of interest: