Yes you can have multiple web applications using to the same application pool.
Is it a performance concern? If it is really high traffic or is faulty code, then perhaps.
Application pools allow pushing sites to different processes, reducing the risk of each affecting the other. If one app pool contains an application/web application that has a memory leak, the leak will only affect that particular process, at least directly. Each process can be recycled either by time or system parameters, which mitigates risks of having something in a bad state.
Performance? Another benefit to app pools is the ability to have multiple instances running simultaneously (a similar thing when putting each app in its own pool). The benefit of this is that more request can be handled at a time. The down-side is that you cannot use in-process session state and your application state will be duplicated for each instance of the process. You would need to consider how much 'stuff' you keep in session and how your caching scheme would be effected, but, it has potential for giving a web application more scalability.
You mention call SSIS... I am assuming that is a long-running service, so you would probably want to push the call to that process to some sort of queue that can process outside of the web service request. MSMQ might work for you. If using a queue as such, you would initiate the running of the code, then have a way of checking on the status of the call to see if it is done.