Bin is a generic extension and can be used by many things across computing.
If you mean the overlay_????.bin and ARM9.bin and ARM7.bin files then not as such -- technically they are the binaries (the code the processor well processes) and though they may contain additional data (I have certainly fished out all types of data from them over the years) they tend not to have an additional filesystem. There are tools to start helping decode them (for a start crystaltile2 features a disassembler window) but that is a different type of hacking altogether.