Indeed, WebKit has been deprecated and won't, therefore, be shipping with the forthcoming Qt 5.6. However, you can still build from source (or, at least, you should still be able to build it from source).
As a general rule, new projects ought to use WebEngine, but because there isn't yet a 1:1 correspondance between WebEngine and WebKit (is there ever going to be?!), you might have no choice but have to use WebKit for the time being.
(I am in that boat too, i.e. WebEngine is currently missing too many things to make it possible for me to drop WebKit -- I tried! --. Yet, I can't see myself building WebKit from source, so I am not going to upgrade to Qt 5.6. In the end, I really wish Qt would release binaries for WebKit. Not as part of Qt 5.6 since it's going to be an LTS, but at least on the side so many people (I am sure) don't feel like their only options are either to build WebKit from source (!!) or stick to Qt 5.5.)