Some reasons I have come across in the past.

Copy process may have hit a lot of smaller files, this will slow down the rate (doesn't seem likely in this case). "Zipping" the directories into one file would prevent this.

Disk fragmentation, disk head has to reseek before reading  new data - this is where defragging the disk can help (doesn't seem likely in this case).

Flow control - The source disk is much faster than the destination, the intermediate buffer fills up and the whole process has to be put on hold whilst the buffer is emptied. Not much you can do but wait. Sometimes slowing down the process can speed up the copying but unless you want to write a script to copy each file seperately its probably not worth doing.

Errors on the disk, cable or bus - corrupted data causing muliple retries (think you would be unlucky if this was the case, bad disk should cause a clicking sound as the disk heads attempt to re-read a sector).

Network sliding window problem - errors in the transmission causes the data to be resent. Initially the data will be sent in small chunks, for each chunk the destination will return a packet to say its received ok. As the transmission progresses if there are no errors early on the chunks become larger to make the copying process more efficient. The problem is if there is an error the larger chunks have to be restransmitted. The are options you can do with network set-up to improved this but  maybe not a good idea to re-tune if this is a one off as it might impact other network peformance. This is more likely when copying files from your PC to an internet based storage.

Sure there are other reasons but retries and flow control are very common.