Nikwax (specifically the wash in type) is what you want to stay away from if your fabric has a breathable membrane. It's wax based so it clogs the pours in the membrane, leaving you to get coated in your own sweat. And it's not as durable as an actual fluoro dwr which means you'll have to reapply more frequently.
That is not really correct. Nikwash, including the wash-in type, is perfectly fine.
Some background: Most factory-applied DWR are fluorcarbon based. A number of re-proofing products (Granger, etc.) also use such fluorocarbons. In contrast Nikwax is a wax-based polymer (but not
actually wax). Both types work just fine for tech fabrics (unlike silicone or simple wax products).
Main difference is that fluorocarbons are persistent
molecules that do not degrade in nature and some have been shown to have carcinogenic properties. Most manufacturers have worked to remove the most problematic compounds (such as perfluorooctane sulfonate (PFOS) and
perfluorooctanoic acid (PFOA)) from their products and/or change to shorter polymer chains (like the C6 fluorocarbon used by Granger).
The basic Nikwax polymer does not have the persistence issue or health concerns. It also does not require tumble drying to bond to the fabric. However, it has been reported to be less durable.
Both fluoro based and Nikwash can be applied as spray-on or wash-in and neither will 'clog the pours' [sic] or affect breathability. The wash-in is slightly more convenient, but there are reports (anecdotal - I have not seen any proper studies) that it does not perform as well as the spray-on, especially for Nikwax. I also prefer the spray-on, because it lets you target specific areas of the garment (e.g., shoulders if using backpack).