Well, any program that compares files and removes duplicates that doesn't look at whether they are links, will remove excess links. By looking at the inodes and device numbers to detect links, you can gain one of two things: have the option to *keep* links - which can be pretty useful for binaries that act different on how they are invoked, or a more speedy comparions, as you don't have to calculate the md5 hash, and then then compare the entire file.