Are there limitations how many layers there should be in a geopackage? It is advantageous to allocate layers into groups to several gqkg, instead of only one gqkg. (I work with approx. 50 layers.)
Looking in the standard I can find only one constraint:
The maximum size of a GeoPackage file is about 140TB. In practice a lower size limit MAY be imposed by the filesystem to which the file is written. Many mobile devices require external memory cards to be formatted using the FAT32 file system which imposes a maximum size limit of 4GB.
So you should be fine.