The HDD does not have an exact transfer rate, it depends on proper maintenance, ie that is not fragmented, nor has bad sectors, etc...
If HDD is SATA 2 and it's the same partition, it's only the speed of data transfer.
If there are two partitions in the same HDD, it is not required this data transfer between the bus and motherboard, ie it loads into the buffer. (then depends of hdd buffer size.)
But for every file copied, the system must keep its index in the HDD's MFT (Master File Table), which makes the copying process slower if you copy many files. And if you have any anti-virus, it will scan each file that is copied.
And if you have enabled the microsoft search file indexing (or any other file indexing service), the result will be worse.
I think there must be many other reasons why the copy of many files is slower, but these should be the main.