Yes. This hack will not prevent any applications from working. The only time that MIGHT happen is if a firmware update gets pushed out, HENKaku isn't updated for it, and your application requires said update - in which case you will have to make a choice between Netflix/other online app and HENKaku.
I don't think it works unfortunately due to the Vita's infrastructure. You're going to have to uninstall and reinstall whenever you want to update to the newest nightlies as far as I know.
Seems to be working for me at least.
On the topic of mGBA, is there a way to make it remember a directory to default to? Kind of annoying to have it just go right to ux.