Clobbering of the Nav menu is clearly a significant bug and will be fixed.
As you noted, the short-term fix is to go in and re-scope it manually. People who have customized their default nav menu in search or elsewhere typically won't be affected, which is probably why it wasn't noticed sooner.
Much of the global exporting is quite intentional. We have users who want access to OSSEC information through the search app. That includes saved searches, views, lookups, and search commands (i.e., most of the app).
Regardless, the scoping is something that has been on the radar to tighten down, or possibly provided as an install-time option. It's a significant enough change that it won't be done before th a 1.2 release of the app, which will hopefully come reasonably soon.
Setting the Nav menu aside, as you noted, there are a few cases where this sort of thing crops up elsewhere, particularly for saved searches and views. Any app that needs to share elements outside itself has this problem, and is going to pollute other app menus. For now, the safest approach is for any app other than search to be very specific when defining its own nav.xml.
I've been meaning to file an ER to ask for a way to scope across multiple apps without resorting to global. Perhaps you and any others who've been bitten by this could make a similar request?
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