I think Bower was just a "good enough" solution when Purescript was initially implemented. Afaik, people are moving away from it in favor of spago [0] or psc-package [1].
JS' semantics are pretty much opaque when staying in Purescript. Of course all bets are off when using the FFI, but then again the same goes for GHCJS.
One major thing in favor of GHCJS is the ability to share code between backend and frontend, but that's not a concern when e.g. the backend is written in another language anyway.
EDIT: Also, Purescript on the backend (targeting node or native code) is slowly becoming a thing as well, as this is what this submission is about :)