JFS is quite a bit faster, supports a much bigger cache, has large file support, doesn't have the 64GB partition size limit and usually chkdsk runs much faster after a crash or power failure and at the worst, the same speed as HPFS.
It also has better NLS support being Unicode underneath whereas HPFS is code page dependent and if you screw up and mix code pages, you will have problems.
I haven't lost a JFS partition yet. Had some break with the worst one where chkdsk or fsck on Linux wouldn't finish, I mounted it read-only under Linux and copied everything but one sub-directory to a different partition. The lost sub-directory wasn't important and I did know the name so could have reinstalled.
There's other times that I've needed to run fsck on Linux to recover OS/2 JFS partitions and in the case of my backup media, USB drives, it is quicker to boot to Linux, run fsck, which under Linux runs the simple log redo that runs during boot on OS/2 and takes seconds. A long chkdsk on a USB 1TB partition takes forever it seems.