I think "Hate Crime" status is necessary in order to offer additional deterrent of persecution of a group in extreme danger of violence, and prevent extremely unstable malcontents from seeking out members of that group to harm.
No one should ever have to fear for themselves because they're different. Personally I think a crime should be a "Hate" crime if it can be proven that perpetrator did it because the victim is/was uncommonly different from them. I.E, Being of a different race, creed, nationality, origin, religion, gender, Sexual Orientation, Gender Expression, having different Medical needs, physical attributes, mental capabilities, or anything like that.
If it can be proven that a crime was driven or motivated by hatred or dislike of something protected, then yes, they deserve a slightly heavier sentence. People with stubborn or irrational hatred or dislike for something can be pretty dangerous, and even more so if they believe what they hate is evil or wrong. So just putting them in jail for the normal amount of time might not be effective. I think people like that shouldn't be released until they're good and ready to realize the misdeed they've committed. If they don't, they can sit in jail as long as it takes, within reason.
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On the flipside, proving that a crime has been committed out of hatred is like trying to hold water in your hands. It's tricky. Generally speaking, unless you've got Audio, Video or written proof of someone basically admitting their hatred...you don't really have a solid case. It becomes a bunch of "He said"/"She Said" unless you can gather enough credible witnesses, and even then it can be difficult.
It's essentially difficult to prove outright without hard evidence of the type which is difficult to legally obtain in a fashion that wouldn't be thrown out of court.