There are no rigid limits to the SOAP message size or the number of documents that can be sent in a single JobSubmit. We do not impose a timeout via our web service, although other external components of the system (proxy servers, etc) may impose limits.
However, there are some Best Practices that we recommend. Since the larger the message, the longer it will take to send and to process, there is little advantage to including more than one document set / destination set per JobSubmit. That is, if you have separate documents to separate destinations, it is best to create separate JobSubmits. They have a better chance of getting distributed in parallel, therefore shorter delivery times.
If you give us some more details about your application, with some specific numbers and possible trade-offs, we can be more specific in our recommendations.