It's important to note that hashes are an extremely flawed method of verifying the legitimacy of an app. If a hacker has managed to replace the app on the website, it's not a stretch to imagine that they have also replaced the hash on that same website.
Not to mention that an SHA1 or MD5 hash cannot be considered to be a guarantee, since it is now possible to create different files designed to have the same hash. All it takes is processing power, and the power needed can be easily purchased from Amazon, or obtained by a hacker by employing an existing botnet.
Code signing is the only way to guarantee that the app has not been tampered with, and HandBrake is not code signed. So it's really very difficult to determine whether you have an un-tampered copy of the app.
Some have pointed out that Apple developer certificates can be purchased for $99, and used to sign a malicious version of an app. This is true, and it's been done. That's what happened in the case of Transmission's hacks. However, this is an easier issue to spot, if you know how, as the code signature will change. If the app is signed with a cert belonging to someone other than the developer, you know there's a problem.
Of course, the average user won't know how to check that - or even that they should - any more than they'll know to check a hash.
Those asking how they can trust HandBrake again are asking a good question. It's particularly concerning that there is a historical connection between Transmission and HandBrake. I don't know how many people may have access to both projects, but these repeated hacks start to seem like an insider job. Without code signing, there's really no way we can be expected to trust HandBrake in the future.
(Fortunately, I only have HandBrake installed on an older Mac with no PII... but even so, this is something that could have infected my Mac, and I'm a security researcher!)