You aren't necessarily slowing down the application by doing this. You are forcing it to run as a 32bit application.
The largest disadvantage of this is that you will be restricted to 32bit memory addressing - which typically (in .NET) means a limit of around 1.2-1.6gb of memory usage before you get out of memory exceptions.
Technically, you may be causing some minor speed loss, since x64 does provide a couple of extra registers. Mathematical operations can be slightly faster in this case.
However, if this is a typical business application, there will be no practical difference. Most of the time spent working in most applications is time waiting on events - ie: waiting for user input, networking events, etc. Those will be identical.
Reed Copsey, Jr. -
http://reedcopsey.com