I can't recall having any problems using
calibre:// URL links when a search or VL is active.
I have hundreds of 'books' linked with within the same libraries and between libraries. Within libraries I use the 'show-book' and 'view-book' directives, sometimes both; and between libraries I use the 'search' directive.
I store the links in long test columns, and the Link column of the authors table (Manage Authors).
For me the addition of support for a 'calibre' protocol is the most useful new feature that has been added to calibre since I started using it over a decade ago. That's probably because I cut my teeth on IMS and IDS TP systems that used network databases.
FWIW - It would be useful if the link tool in the long text editor (LTE) had a widget to get a calibre:// URL as well as a file:// URL, e.g. an additional "Choose a book in your library: Browse (button)' widget. It would avoid having to copy the link from book details before firing up the LTE and pasting it there.
It would need a means to select a 'show-book' or 'view-book' link… radio buttons? And for me at least browsing the library folder tree would be fine, for show-book one would select the book folder and for view-book the format file.
BR