What you are seeing is usually related to how colors are assigned in Inventor and what DWF export actually includes.
In DWF/DWFx export, Navisworks reads appearance mainly from the component/material level. If colors were applied as assembly overrides (for example using Finish/Appearance at assembly level), they are not always written into the published DWF unless those properties are included.
Two things to check:
First, in Publish → Custom → Properties, make sure appearance/material related properties are enabled. In some Inventor versions the option is shown as Material rather than Color/Surface, and if Express publish is used these properties are skipped.
Second, verify how the color was applied. If the subassembly color comes from an assembly-level override (component color), it may not transfer reliably to DWF. Assigning the appearance at part or subassembly level (not only as override in the parent assembly) usually exports correctly to Navisworks.
So in practice the most reliable workflow is: apply appearance in the component itself (or via material), then publish with Custom properties including material/appearance. After that the colors should appear in Navisworks.