There are no issues as far as we know using Aware IM with version 5.0.
As far as the difference between MySQL 4.1 and 5.0 is concerned, we can't tell you much beyond what is written in the MySQL documentation.
There was a big difference going between 4.0 and 4.1 (support of sub-queries) which is very important for Aware IM, but in 5.0, as far as we know, there were no changes that are significant to Aware IM.
So the best thing to do is read the list of changes from 4.1 to 5.0 on MySQL web site and then decide whether these changes are relevant to your environment.