First, reverse engineering in some cases may violate the DMCA regardless of what you do with the code.
If a patent is valid, then reverse engineering doesn't get you anywhere. Patent is not copyright. You can sit down and write your own implementation of the code, not copying anything, and still violate the patent.
Most of the people who complain about having to pay for exfat are the open source people who are used to getting what they thought was free software. However with the Heartbleed and shell shock issues this year the crditbity and false notions that open source are free are going down the drain. Meanwhile, Microsoft successful defense of the vfat (long for name in fat32) and mapping parents against Tom Tom has minimized cases where someone goes against those patents and almost all major distributions of Linux will not (and probably can't) add exfat to the distribution. That leaves most using FUSE and there are many complaints over the various forums about issues, bugs, and corruption ISO g the FUSE drivers.
There are at least 4 patents involved, extensible file system, name hash lookup, transactional fat, contiguous file allocation. If you look at overcertified'a recent slideshare presentations on exFAT, including the recent HTCIA 2014 exFAT presentation, the patent numbers are listed on the ending reference slides.