No, that's not what it means. :) The language says that "it" was "very enjoyable". That fact is not altered by the rest of the sentence. The "if" and the "rather" do NOT represent any kind of condition or subjunctive mood related to how enjoyable it was. It was very enjoyable, that's a fact. The sentence does NOT mean "It would have been very enjoyable if it hadn't been lacking on the practical side." What it means is "It was very enjoyable. Now, I must also point out, though, that it was very enjoyable despite the fact that it was rather/somewhat/very/quite lacking on the practical side". "the thing was <X>, if rather <Y>" means "the thing was X EVEN IF YOU WOULD AGREE WITH ME THAT it was <Y>". That's what the "if" means. It's not the clearest way to express it, but natives are used to it. Now, that's what the sentence means. You could then creatively infer that had "it" NOT been rather lacking on the practical side, then the writer would have found it even more than "very" enjoyable. That's a reasonable thing to infer, and it may well be true, but the sentence doesn't say that, and it's not the concept it's trying to convey. This is a half-glass-full sentence, not a half-glass-empty one. :D

In a nutshell, yes~ if the activity had a practical side to it, it would have been even more enjoyable. If it is lacking a practical purpose, it is just very enjoyable.