Same here in principle; the problems start when you have big project which require qmake SUBDIRS and the like; it's ugly and very slow. I'm neither one of the 'cool kids' ;-)
You can also easily run into that as a solo developer if you have a project with more than one target, e.g. an application with a few shared libraries (or e.g. Qt plugins).
> is slow to modify a qmake file with subdirs, or slow for qmake to evaluate it?
It's mostly slow because it generates a lot of make files which all have to be run to find out whether there is anything to do; you can e.g. try by generating the qmake project for LeanQt and open and run it in Qt Creator; then when everything is built make a change in one file and build; when you do the same with LeanCreator and BUSY you will notice that it's more than twenty times faster.