Hacked application are frequently infected - a good reason to avoid them (aside from the legal reasons).
Hacker tools are also suspect, since someone who is hacking is often (but not always) involved in activities that are questionable at best. A would-be-criminal is a good target for an already-is-criminal.
That said, I share your frustration when using legitimate tools for legitimate purposes and having them flagged as malware. For example, the highly-respected site, www.nirsoft.net has a tool, Produkey, to show the Product Keys for software installed on the computer. While it can be used to steal a product key, it does nothing bad to the computer and certainly has legitimate uses, like when you need to re-install software, but don't have the product key sticker handy (or it's worn off the bottom or your notebook). My anti-virus flagged it until I added it to the exclusion list. I felt safe doing that because of Nirsoft's reputation.
Bottom line - it's best to stay away from software used for shady activities, and cracked, hacked software and keygens. They're often infected with viruses or spyware and your antivirus is right to call your attention to it. (Not to mention the attention you may attract from law enforcement folks.)
If you have a legitimate software from a reliable source and you are certain it has not been infected along the way, you can tell your antivirus to ignore it.