I agree with Terry on most points and a qualified agreement on one other point.
If you have already decided you prefer the scale Kadee couplers, you should get into practice of installing them. Since the beginning of Kadee, scale hobbyists have made it part of their regimen -- especially in HO scale during the horrid time of X2F horn-hook couplers.
I think it was Jack Wheelihan (hot water) who said he has got the conversion process down to 10 minutes per car. He may have shims already standing by for conversions, but regardless the process becomes routine.
As to why manufacturers haven't uniformly created mounting holes and cast-in top frames for Kadee couplers, I'm guessing it because they are reluctant to retool older pieces. But that doesn't explain newer models.
As for cutting off the traditional couplers, I think Terry is right. If you decided you prefer scale couplers, it shouldn't matter to you.
However, on the issue of resale, if that is your concern, I would set aside the argument entirely. I like the traditional couplers, as do most others, so I wouldn't consider buying converted cars. That could affect market value as a whole. But, frankly, it's time to stop thinking about resale value anyway, especially for non-Lionel cars.