It's claimed grep is "well named" because even though it's not obvious when you first read it, that it being a contraction for "global reg ex print" and hence memorable. I'm not sure the same argument can't be made for libsodium which assuming the reader is familiar with NaCl (the same as the assumption that the previous reader is familiar with regex) then it's an equally memorable name for your crypto library.

There's always a consideration about the context the name is intended and likely to be used in. The article mentions engineering naming and "ibeam", but engineering has it's own technical names an jargon as well. Most people wont know what "4130 tube" means, but people who build bicycle frames or roll cages will - and they're likely to use the less specific term "chromoly" if the don't need to distinguish between 4130 and 4145.

In my head "libsodium" is similar - if you don't know what it (and NaCl) mean, you 100% should keep out of that part of the codebase.