On linux, here are the contents of ~/.vkquake:
.vkquake
├── ctf
│ └── pak0.pak
├── dopa
│ └── pak0.pak
├── hipnotic
│ ├── music
│ └── pak0.pak
├── id1
│ ├── music
│ ├── pak0.pak
│ └── vkQuake.cfg
├── mg1
│ └── pak0.pak
└── rogue
├── music
└── pak0.pak
Running vkquake with just vkquake starts id1 as expected, and using vkquake -game dirname works as expected.
If I remember right, placing everything in this directory used to show the folders in the mods menu right? I could only get them to appear when I used vkquake -basedir ~/.vkquake.