The number of vassals depends partially on the level of centralization of the realm in question. In CK3, this is affected by Crown Authority, which on the whole tends to be higher on average than the old CK2 centralization laws, which may be why you notice less vassals in CK3 conversions as opposed to CK2 conversions.You could just set yourself to convert as the HRE and annex the lands you wanted to keep via console. Or release the areas you want to be independent in CK and then use console to make them subjects in EU4.
In any case, weren't strong vassals supposed to be vassals in EU4 by default?