Portage assumes that all relevant system-wide files are known to it, by way of installing them through it (or a compatible tool that would also register the files in the package database). Further, it assumes that files it installed were not silently changed by other programs. If you install an npm package system-wide, you risk three things:
It installs a file that Portage is not expecting, which may lead to spurious dependency problems later.
It overwrites a file managed by Portage.
It is not managed by Portage, so future upgrades/removals are your responsibility, not Portage's responsibility.
If you are willing to deal with those risks, yes, go ahead.