About 95% of the code I write with JUCE is written as modules (i.e. as potentially re-usable code not tied specifically to one project), and I haven’t found it to be inconvenient.
My workflow is that I work entirely in IDE (read: I never use the live build engine), and edit my module code directly in IDE via the referenced files. I’m not quite sure what you mean by “They’re in an included folder”, as I can see them just fine as source groups in Visual Studio (haven’t checked Xcode recently).
Whenever I need to add/remove a file, I quit my IDE, do my changes of actually adding/removing the file from disk and from the module header(s), then re-export from ProJucer and continue working (it’s not nearly as slow/nasty as it sounds).