Unfortunately, single-pin Molex housings do not exist. If you look at Molex’s page for SL crimp housings the minimum number of circuits is two.
When I need a single-pin housing, I either use a 2-pin housing, or just put some heat shrink around the crimp, depending on the application.
For the housings, Digi-Key is marginally less expensive, unless you’re buying female housings in quantities of 1000 or male housings in quantities of 300. For the pins and sockets, Hansen is less expensive than buying the comparable part at Digi-Key, but you can save money by going with the tin-plated versions available at Digi-Key.
Certainly a reasonable way to go - I was thinking about making one possible “starter kit” option for teams that want to plan to use three pin connectors everywhere to keep things simple and minimize cost by buying in bulk.