Do you mean slots in SIW itself? I guess you talk about simulation complications. I think prototyping can help.
Currently i want to learn SIW by ordering some SIW test PCBs:
1) make pcb layout with long SIW, put different slot configurations on it's top (without green mask!)
2) order board (online pcb manufacturer, etc.)
3) choose slots you want to examine, solder copper foil above unused slots
4) after examining some slot configuration, put copper foil above them, and check other slots by unsoldering foil on top of them.
In my case i want to try SIW filter: i make long SIW with different shapes on ground plane (removed copper). By adding foil i can choose different shapes and check filter performance. You can order prototypes too, and then alter your simulations in right direction.