"libsodium" is just NaCl with autoconf cruft added.
NaCl does not use autoconf nor even make.
It is not necessary but if someone really feels compelled to use it, why stop them?
I have never seen any author or end user comment that they dislike using autoconf, or write alternatives to it. Autoconf is loved by all, isn't it?
I think what you could say is that using NaCl in your own software is the only way to get good at using it. Maybe the existence of libsodium means that more developers will have a go at using NaCl? Is it easier to use than an SSL library? The only way to find out is to try both and compare.
There is no need to use autoconf to build libnacl.a. The original build system for NaCl is beautifully simple. But if someone misses autoconf and make, then libsodium has added in those dependencies.
More projects using NaCl:
As far as I can tell, the authors listed on the above site are not "rolling their own crypto" for their projects, they are using cryptography written by the author of NaCl.
Personal bias disclosure: I find NaCl easier to use than all the SSL libraries I have tried. If I am not mistaken, I believe this was a design goal by the author.