To disable in Nintendont you force Ntsc or Pal60 video modes and it's gone for most games. A few ones will require to modify the iso liie soulcalibur 2.
In my tests pretty much all games work with either of the 2, regardless of region (and PAL games have 60hz support or are modded to play at 60hz).
The "downsides" of removing deflicker I can think of are an actual one and a "matter of taste" one.
If you play at 480i, so no Progressive Scan, depending on what TV you are using you will be seeing the flicker. Basically you will see the screen shaking a bit, which is exacly why the filter was made in the first place. It can strain your eyes and with certain color combinations it can be very visible.
This, of course, does not happen on Progressive scan.
Playing on hdtvs, they tend to have their own filter for interlaced content (depending how you connect them, it might not happen with digital inputs like hdmi) so you may gain some sharpness by taking it out as you would get twice the filter. On CRTs it can vary a lot.
Besides that, a few games use dithering to attempt to give more depth to the picture, and removing the filter will make it more aparent. In said cases, you can just make the loader use a less strong filter so you gain some sharpness but without going all in to avoid it.
Because pretty much all third party games use the strongest filter (default option on the sdk if I remember right) by using a lighter one you still improve the picture.
There's really no downsides besides the case of 480i. Now if someone would rather have a blurry picture over a filterless one it's entirely their choice.
About the deflicker in emulators, I would bet they use the lightest filter mode, and no the stronger ones. Retroarch does for example.
I assure you only a handful of games use the less obnoxious ones, selected first party games. I checked well over a hundred games when this was being researched and was a bit sad to realize devs probably didn't even care one bit about changing or removing it.
Except HAL Labs, which took it out for games like Brawl and Kirby's RTDL. Good guys, know what they are doing. GoodFeel might also have not used them, if I remember right.
TLDR:
There's no reason to have the filter with Progressive scan unless you want blurry picture or as mentioned, camouflage dithering which you can still use a weaker filter and gain sharpness.