Modifications of any type
Detract from the value - as a collectable rifle. If you're selling it as a shooter, it might add some. (94s being light rifles, they kick some.)
However, that rubber butt cannot be 'fixed' by simply replacing the stock. Yes, there are replacement original stock butt pieces which will replace the current one. However, that doesn't make it original, it makes it a 'restored' or 'refinished' rifle. You probably won't make it worth any more than it was with the rubber butt pad.
If you can show the history of the rifle, those modifications could actually enhance the value of the rifle, but not always.
Probably the best way to get an idea of the price is to check on some of the websites selling guns and find comparable pieces. One also has to adjust for locality; different guns sell for different prices across the country depending on local demand and local 'styles'.
That is a neat old rifle and still has lots of use. If nothing else, it's a nice bit of deer hunting history.