As others have pointed out, it's not really frowned upon as much as it is inefficient for certain missions. It takes a small amount more delta-v to get into than an equatorial orbit and it's harder to rendezvous to a polar orbit than an equatorial one.

The bigger issue is on interplanetary transfers. A polar orbit means that your velocity vectors (ship relative to planet and planet relative to star) aren't parallel, so your star-relative velocity is quite a bit lower, meaning you need a bigger transfer burn to reach your transfer orbit. On top of that, the planet relative velocity vector is large enough to give you a seriously inclined transfer orbit, which can cause you to need expensive course corrections.

Kerbin's orbital velocity, according to the wiki, is 9284.5 m/s. A normal orbital velocity for Kerbin is about 230-2400 m/s. So, in an equatorial orbit, your peak star-relative velocity is 9284.5 +2300 m/s, or 11584.5 m/s. In a polar orbit, your peak star-relative velocity would be sqrt(9284.5² + 2300+2) m/s or 9565.14 m/s. Now, the oberth effect means that the transfer burn wouldn't need the full 2019.36 m/s compensation, but it does still mean that the transfer burn would have to be larger, hence less efficient.

I'm not sure how much this affects travel to the Mun or Minmus, as it won't affect the transfer orbit burn, but it will affect the capture burn since the ship's velocity isn't parallel to the target body's velocity.

But, as others have pointed out, polar orbits aren't frowned upon for those missions that they're appropriate for. In fact, in career mode, my first mission that I plan on doing EVA reports during is always a polar orbit, just because without a near-polar orbit, you're going to miss a few biomes (assuming that you can't still get tundra biome science in an equatorial orbit, but that could easily be a bad assumption).