Is it harder for academics to make fundamental discoveries than in the past?
Actually, exactly the same question might have been asked around 1900 when Henri Poincaré ruled the world. 

There is a tradeoff, of course. Some fields get saturated and the seemingly important questions get answered, closing the field in some ways. But those fundamental breakthroughs may open new lines of inquiry. And there is the corresponding effect that other fields open up. Mathematics is like the latter. People today think about a lot of mathematical ideas that didn't really exist historically. 

Whether physics is a fixed field in which everything will eventually be known is, I think, an open and debatable question. I suspect that there will be new ways of thinking about things and thus new and important questions as long as humans can manage to still exist. Quantum entanglement is still pretty "spooky". 

And in the social sciences we may be only at the beginning of what can be known. 

Moreover, each new generation of scientists, in whatever field, starts out at a higher level than their predecessors, and so, have a base on which to reach still higher, with a deeper understanding. Poincaré had problems grokking relativity, as did many of those in his generation. After they started to actually die, relativity came to the fore.