Will installing a silicone sock on my Nextruder affect the input shaping  

RE: Will installing a silicone sock on my Nextruder affect the input shaping

No.

Long answer...
The amount of mass added by the silicone sock is absolutely negligible for resonance. Even if it were, the effect on print quality would still be negligible. If you really do care about this though, I would recommend doing your own testing right now without a sock, and calculating the resonance value. Compare that with what the factory default is and you'll probably find that it's already quite a bit off. A few grams difference on the nozzle isn't going to make any noticeable difference.

The real difference you will probably see is in temperature effects. The heater block should maintain a more constant temperature as it's being insulated from convection cooling. The nozzle->part interaction will also slightly be obscured by the sock unfortunately, just due to the fact that the sock interferes slightly with the airflow.

From personal experience, it's a worthwhile investment. PLA would be the material with the most potential for negative effects, but so far it's performed flawlessly. A lot of people will hesitate to recommend a silicone sock in general just due to the potential of the "blob of death" (filament getting trapped inside the sock, resulting in a solid plastic encasement of the entire hotend assembly), but the design of the MK4 mitigates basically every aspect of it.

RE: Will installing a silicone sock on my Nextruder affect the input shaping

Make sure to turn on the sock setting in the hardware settings menu

RE: Will installing a silicone sock on my Nextruder affect the input shaping

I was never a fan of silicone sock for the MK3 due to the design of the V6, where the sock was very poorly maintained.

On the MK4, the sock is very well held in place, and if like me you print a lot in PETG it’s really worth it.