If you do a hot cloning (while physical machine is running during migration), VM converter will install an agent on your physical machine but you can automatically uninstall it upon finishing the conversion process or do it manually. Apart from that, there's no other modification whatsoever will be made on the source system.
During the hot cloning, there will be a lot of network streaming from your physical machine to destination host. Also converter agent will read all the blocks on your HDD of source system. So these are the side effect when doing the hot cloning. So to sum up, your physical source machine will be effected in terms of CPU, Memory, Disks and Network contention. From my past experience, most hot cloning of Windows boxes are fine since they are under utilized most of the time.
Hope this helps.