Someone who spends 99% of the time monitoring an autopilot will almost definitely not have the same hand flying skills/currency as someone who never uses one, but as to whether or not the autopilot hours should be logged - it could get really nitty gritty.
I used to fly airplanes some of which had working autopilots, but the things were SO liable to under perform or malfunction that you had to monitor everything just as closely as you would from flying without it and be ready to intervene at any time. This is very different (technically it shouldn't be but being real here) from the autopilot on a modern jet aircraft (as an example, I am sure many lighter aircraft have good automatics too) in which you could engage it after flap retraction and then go to sleep until time to configure for landing more or less, perhaps waking up to reset the MCP at top of descent.