Please tell me what prevents you from copying the regular file “pak1.pak” and renaming it as you need. Open it, delete everything unnecessary from it and copy the new contents inside it and then save the resulting pak archive? I used to do this and all the problems were solved.
.pk3 files are simple .zip files but renamed. They appeared in use starting from Quake 3 Arena (Quake II still used .pak files). I don’t think vkQuake supports those, and not all variations of Quakespasm do actually - I think only Quakespasm-Spiked does because it has a lot of features from FTEQuake.
How do you want to modify the HUD? The graphics for the elements of the HUD is in the gfx.wad file if I remember correctly, but the way HUD actually works is one of the things that is coded in the engine and it’s pretty much unmoddable unless you are using CSQC, which again, not every engine supports.
Good point though with the “.pak” and “.pk3” archives nonetheless - the “.pak” extension, should be done something with; it is an obstacle for a lot of potential modding, unlike the “.pk3” or other “.zip”-compliant files, which are mostly user-friendly and easy to deal with through basic system utilities.
EDIT:
Unless you argue that modding should only be left to those who know what is what or are willing to go quirky ways with very obscure toolkits.