When I was at the Manchester Play Expo event last year, I had this discussion with the guys on the AmigaKit stand - the general thought is that whilst the ACA500 may work on the A1000, it could "cause damage" to the ACA500 due to timing issues. They weren't much more specific than that to be honest and I've not found any evidence to either confirm nor deny these claims.
However, when I tried it on my A1000, it did NOT work ...... mind you, nor did my bsc Alpha Power IDE controller, so not sure if the expansion connector on my A1000 is the problem here.