Well, a pro might be (and I'm really looking at this from an optimistic perspective) that they recognized that the standard libraries didn't fit their needs and they created their own tools, which could mean they have skilled developers that you can learn from.
If you are going to work with and program against these custom libraries, this will help you improve your skills and get a better grasp on the problems these libraries solve.
The obvious downside is that you will have to learn to use and program against these custom libraries, a skill you won't be able to use when you move on. This gives you that nagging feeling, which I find really really annoying. The -"why am I learning this, I'll never use this stuff again, I have better ways to spend my time"- type of feeling.
Final point: software organisations (and their clients) do work with the standard libraries like Spring and Hibernate, so it's a good thing to have them on your resume, which is something you won't be able to do if you are working with a custom set of tools.