As of yet there is no “official” support for a project spread over multiple PCB’s, but it is a recurring topic and it can be done.
https://forum.kicad.info/search?q=multi%20pcb%20project
I also once did an experiment (no real PCB) in this direction, and it all seemed to work just right:
Apart from that, there are significant differences between a schematic made for simulation, and a schematic made for PCB design. For example for simulation you usually do not bother much with voltage regulators and connectors. Simulation is typically also done on relatively small parts of a project, such as an ADC front end, a HF mixer or other small identifiable block.
In my “multi PCB Project idea” I used a hierarchical design, and multiple sub project to organize different sheets for the PCB’s. Maybe one (or a few) of those can be tailored for simulation too. Or else copying parts of a design between a “Simulation Project” and a “PCB Project” is quite easy and straightforward.
Also, schematic entry is a relatively small task. The time consuming part is in the design itself. Reading and understanding datasheets, comparing specs of parts and figuering out what to make in the first place.