If I have a paper wallet that has .001 btc, could this be worthless in the future because when I sweep the funds the fee is so high?
It shouldn't matter if you are using a wallet that gives you manual control over the miner fee that you use to sweep the paper wallet. You can set it low and then use RBF to slowly increase the miner fee if it sits in the mempool for too long for your liking. If a miner feels like it is worth it to add it to a block, then they will add it or you will need to bump the fee.
Furthermore, we are likely to see more scaling methods put downward pressure on the cost of sending bitcoin on-chain. There are currently about
10 methods for scaling bitcoin in practice with multiple more in the works from various companies and FOSS projects. With so much innovation taking place, I am not worried about fees getting too high for making on-chain payments within the next decade or two.