I had a similar question and found the following two helpful resources: the accepted answer here and this video (as well as the other ones on the same site).

In the following answer I'm assuming the Linux file system, because I am more familiar with it. You seem to use Windows, so there could be subtle differences. (The most obvious one: Linux uses slashes /, Windows uses backslashes \.)

As I understand it (correct me if anything's wrong):

• ./pkgs contains all the packages you ever downloaded for any environment (unless you actively delete them of course). This ensures that you don't have to download and save the same package again for another environment.
• ./envs contains your environments (other than the base environment). Say one such environment is called heatwave (others use snowflake as an example, but the times they are a-changin'). Then ./envs/heatwave contains subdirectories like ./envs/heatwave/bin and ./envs/heatwave/lib. (I suppose Linux's lib corresponds to Windows's Library.) These directories contain hard links to the packages associated with the heatwave environment. The files are not duplicated but the hard link makes sure you can also access them from heatwave (and not just from ./pkgs).
• Then there's also the base environment. The associated bin and lib directories are not under an inexistent ./envs/base directory, but instead directly in the root directory of conda: ./bin, ./lib.

In particular, the apparent duplicates you found are in fact hard links to the same file.

Further info that is not directly related to the question but may help you understand the context: Linux vs. Windows file system, "bin" vs. "lib"