I have about 40 uncouplers connected to my 5 AIU's. They work fine through the remote, however I advise to also wire each uncoupler in parallel to a local pushbutton. Sometimes it is cumbersome to use the remote, when you are also running the engine. this is also handy when having guests "help you out" on the layout.
I had a number of uncoupler tracks overheat and melt because the Lionel supplied pushbutton stuck in the ON position. I recommend using a purchased, higher quality pushbutton instead of the plastic one supplied with the track section. However, I have only had maybe 5 pushbuttons cause problems out of the 40 that I had, so you may be OK. Keep an eye on it to be sure the button doesn't stick.
I also had one AIU ACC port "stick" which also melted one of my uncouplers. Apparently ACC1 and ACC2 can stick ( a software problem I was told) in the older versions of the AIU. I only had this problem with 1 of my 5 AIU's. The solution was to not use ACC1 or ACC2 for uncouplers.
I also modified my uncoupler track to have a red LED light illuminate when the uncoupler was receiving power. This was done to help with the operations (as you can see if you are powering the correct uncoupler before the uncoupling thumb tack goes over the magnet). I was becoming paranoid, since I had lost 4 uncouplers so far (a $125 value), and wanted to be sure I did not continue to have these problems. If you are interested, let me know and I will post the procedure and parts required to modify the uncoupler. It is reasonably easy, although you need to do some soldering (which I am not very good at, but still survived it)