Sawdust irritates their eyes, and the lemon scent might make things worse. It isn't natural lemon scent anyway, it is some factory made smell. I use hay and straw in my litter boxes, and newspaper underneath. If cleaned out regularly, bunnies don't smell bad, and if they do, then it is usually from the food. Excel pellets make them smell worse than other pellets, and some vegetables can have a similar effect. A little bit of smell is normal, if you can't bear that, then house bunnies are not for you.
If you are worried about flies, you could get a mosquito net for the window. It is very rare that a healthy rabbit with clean fur gets flystrike. But mosquitoes can come indoors and pass on myxi, too, so if you have many in your area, a net is a good idea.