Are they intended to be used by the IDEs only?
No. Though the strong point of CHM is the index that makes quick lookups easier.
The HTML and CHM docs also show more source detail than the PDFs.
When I open toc using hh.exe, it shows nothing.
Yes. toc.chm turned out broken. Don't worry, it is a autogenerated file, and does nothing but provide links to the TOCs of the other CHMs.
TOC.chm is mainly used to avoid a limitation of the textmode IDE (that it can only have one TOC in total, not one TOC per file), and has no relevance for Lazarus use.