Yes, of course
You add a romfs subfolder to a title's folder IF you want to add/replace files in the romfs, else you don't need one
You add a code.bin/ips (only one) to a title's folder IF you want to replace/patch its decompressed executable, else you don't need one
You add a locale.txt (with the appropriate contents) to a title's folder IF you want to do language/region/country/state spoofing, else you don't need one
Luma does not support a romfs.bin archive, only extracted files (which last time I used Pk3ds it did leave in place... in any case, it's simple to extract again with 3dstool)
The biggest limitation of pk3ds is that it doesn't readily allow you to identify only the files that were changed (so that you can waste less space due to effectively having them twice), but that's another point...