There are only 2 ntr scenes, both with Grace.
The first with James has no influence as far as i know, as it is one time reward for him and before she even meets the MC.
The second scene u can offer her as payment, which is basically her job. I never tried that option myself, but at least she is very gratefull if u protect her, so it will maybe slightly impact the relationship with the MC.
But the larger impact is likely with ur boss, as he is pissed of how u protected Grace...
more games with avoidable ntr should have the option to shoot the guys which wanna bang ur girls 
.