What information is available about these file formats? What tools are available for parsing these files?
The new version of the Simulink Library for Java has full SLX format support. The documentation is not explicit, but the source code contains all details for parsing it.
As answered by rob, the Simulink Library for Java supports Simulink's MDL file format and also can parse the Stateflow content. The library is Open Source, but the only documentation is the source code.
We are currently (as of September 2014) working on SLX support and expect to release this in the next 1 or 2 months. If you need the code before this time, feel free to contact me.
It is true that when using the library, your code may possibly break with a new Simulink release, as the file format is not documented and we had to reverse engineer most of it. However, we are currently actively updating the library in case of problems and with the source code you might be able to fix it even if we are not around.
PS: I would have posted this as a comment to rob's answer, but it seems I do not have sufficient reputation to do so :(
Disclosure: I am one of the developers of the mentioned library.