Great question — answering as the UphillTech team:
Yes. It depends. From search engines point of view it would be one site. If content between two installations is grossly different that likely won't be efficient for combined site outlook. I'd prefer site1.example.com and site2.example.com if hosting two different sites on same domain.
Full answer by Rarst: https://wordpress.stackexchange.com/a/1936 (CC BY-SA 2.5).
Need it done for your business? UphillTech.
