Well, I don't use Hex2bin.exe at all since my programmer accepts both .hex and .bin formats.

But if I am not wrong, it can not be Hex2bin.exe which is filling space with zeros. For example if your .hex file contains 240 bytes of code, Hex2bin.exe should generate a binary file of the size 240 bytes. How does Hex2bin.exe know that it should fill in zeros and upto what length?

In my opinion, it is the your programmer's software which is filling unused buffer area with zeros.

As a check you can run the programmer's software and see the buffer to check what it contains. I am sure it muct have zeros.

Many device programmer's softwares have the provision to fill in the buffer with a default value. Check the menues. I hope you can find this setting.