Nuclear weapons were just not developed in time for use in the European war. FDR apparently did think about it in December 1944 but there was just no way to make it happen, since the first atomic bombs weren't ready until the end of July 1945, well after German surrender.

As for other WMDs, the Allies did stockpile chemical munitions but did not plan to use them unless the Germans used them first. The Germans vice versa. This was a deterrent situation of sorts — they both had the capabilities to drop terrible gases on their respective troops or cities so both decided it was not a good idea to go through with it, and both had learned the experience of World War I that gas did not really provide a significant strategic advantage (it just meant everyone had to wear masks and a lot more people died unnecessarily).

US scientists did consider the possibility of dropping radioactive byproducts (e.g. a dirty bomb) on German fields but calculated it would be extremely hard to be effective at this. It would also reveal they were working on nuclear reactors, which was still a big secret.

I do not quite recall whether much work was done by the Allies on biological weapons research — I believe some was, but the specific references elude me this morning. The problem with biological weapons is similar to the chemical weapons issue (deterrence), but also because it is harder than most people think for biological weapons to be effective.

As for other means of "mass destruction" without WMDs, the ruinous incendiary bomb raids against German cities, forests, and farms were intentionally meant to cause mass destruction, mass starvation, and mass casualties. We do not traditionally consider these WMDs, because we have restricted that term to only a few technologies, but it is hard to not mention them when thinking about Allied designs on the destruction of Germany.