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Even experienced NB developers are surprised, when Add Module Dependency dialog doesn't find a module in platform which is disabled in platform.properties (e.g. Visual Library by default). Actually adding the dependency need not to be directly possible, but its public packages should be searched as well and listed with an explanation that module is excluded in Properties -> Libraries. Alternatively there could be a button/link "Include module" in results allowing to either include module directly (+also transitively include dependent-upon modules?) or at least open Properties -> Libraries on the module.
Note that if we did http://wiki.netbeans.org/EnhancedConfigurationOfNBRCPProjects#section-EnhancedConfigurationOfNBRCPProjects-JesseSMoreOrLessUnrelatedProposalForDependencyBasedModuleIncludes this would not be an issue.