Thunderbird (and other decent desktop packages) allow me to reuse the over a decade worth of training I have with my OS's KB shortcut semantics.
In addition, using the keyboard in a browser is a mess. It is very easy to not have the current context set to a different application, and Gmail's non-standard K/B shortcuts can lead to unpredictable (and destructive) changes in other applications (for example, accidentally entering random text in a document open in my text editor). Using standard OS K/B shortcuts means that if I am doing a search, and even if my current app is not the one I think it is, it's likely to still do a search, and not enter random characters.