The style of scons scripts we use was created in 2001 for an engine we were making for an MMO which eventually became "Regnum Online". I don't remember if there was a specific reason, I probably just didn't like the name "Sconscript" that was on all the documentation (it looks too much like "SConstruct"), so I used the name "SCsub" because it's like a sub-script (or something that goes on a sub directory).
The way we use scons (which is also unusual I think, I've seen very few projects using scons over the years, and they all used it in a very complicated way which failed to build most of the time) remained very similar over the years, in fact it's simpler today. We did env.Clone() a lot more, at some point we built multiple dlls, and until recently we could build multiple targets with the same command. There's still a few things we could improve about it (for example we could put all the .o files in some hidden directory, and I wish there was an easier way to distribute scons for windows), but I'm pretty happy with how it works now (although I would like to still build multiple targets with the same command :p)