Would this not create a huge vacuum leak rendering the vacuum operated slide diaphragm in the carb useless among other problems?
I don't think so; already, vacuum ports operate the petcock, and, on later and California model KLR650s, some sort of pollution control mechanisms.
With air flow through the venturi, "vacuum" (pressure differential) should be available for CV carburetor operation (or else, Bernoulli was just funnin' us). Some sizing adjustment regarding jetting, profiling of needle, slide spring strength, etc., might be in order if any great flow occurs from crankcase to intake manifold, but . . . I'd imagine the flow minimal, for an engine in good condition.
I'd envision the crankcase vent line connection at the intake manifold much smaller in cross-section than the venturi; thus of minor consequence regarding the resulting dynamic vacuum.
Many carbureted automobile engines connect their crankcase ventilation lines to the intake manifold, yet retain enough vacuum for fuel flow. Don't know of any CV engines so rigged, but imagine enough pressure differential exists to exercise the diaphragm and slide mechanism.