If you fill them I would use something like a tinted epoxy. A lot of fillers will come loose with the beating a steps will get. The filler will not make the imperfections go away if that is what you are trying for.
You may want to be careful when applying stain as it can pool in the nicks and leave dark spots, also may not get into the nick and leave it lighter. It can give some character but I still try and get them "right".
there are stainable fillers, usually it is not the water base one, the stinky acetone smell ones in a small can that cost you about $10... Dap Plastic wood... you can thin it a little with acetone to make it easier to apply... smells though.
I have good luck with this one. but require sanding.
Enjoy the DAP 4 oz. Natural Plastic Wood Solvent Wood Filler 21502, stainable hardens to create a surface and body that looks and acts like real wood from The Home Depot