Nope, your spring and Seam code will not be effected. The configuration might be more difficult though depending upon the transactionManager you are using. For example, if you're using a HibernateTransactionManager you need to make sure that both spring and seam are using the same SessionFactory. If you're using a JTA TransactionManager then you shouldn't need to change anything.
Does that help?
I'm sucessfully using SEAM - Spring integration with modular approach to Services, Entities, Business and Web (may be remoting / webservices later).
If you get any problem with configuration just post it here, i'll try to help you.
What I don't understand is:
I inject Seam managed Hibernate session object via @In
What is happening when I configure Seam to use Spring managed transactions (PlatformTransactionManager)?