Are there any known issues around multi threaded invoicing using 2 AOS instances in MS Dynamics AX 2009 SP 1 ?

There are no known issues currently in terms of the technical reliability of the AOS being able to handle multi threaded batch tasks. What is important here is that you review/ check the X++ code in terms of being ready to really benefit from running in a multi threaded batch task. The following blog post explain more in detail what I mean here: