How to reduce the number of files in the anaconda directory?
Anaconda uses hard links to reduce the consumed disk space. But if a limit is imposed on the number of files, each hard link counts.
As discussed in the comments, using Miniconda instead of Anaconda, and installing only the packages you actually need, might help.
If this isn't enough, I'd recommend to merge several of your environments into one. Then you'll have fewer hardlinks for the packages that overlap. Of course that is the opposite of what environments are there for, but such is the nature of workarounds.