I can more than counter Wobbuffet, I can instantly win games if you use Wobbuffet. Substitute, Calm Mind, Psychic, Thunderbolt Gardevoir @ Salac or Leftovers. Or you could add Pursuit to something like Tyranitar and do ~70% to it, meaning it can't really come in on anything ever again.
You could use the same argument for Dugtrio being uncounterable, because you can't switch in on it.
Well for one, no sane person will use Substitute on Gardevoir except for the specific purpose of "countering" a Wobbuffet that just went and killed something on your team. It's a very specific, limited counter, along with its lesser cousin, Sharpen Porygon2. ;/ Obviously it can't Mirror Coat Dark pokemon or Counter Ghosts, but neither of those are particularly common (Dusclops sometimes has Shadow Ball, Gengar rarely, Seismic Toss or Night Shade will take ages to kill Wobbuffet; Dark is basically reserved to Boah or the rare Houndoom) and they can't actually switch in to Wobbuffet until it kills something already (then runs off, which only Pursuit Houndoom can do much about) or sets up free turns with Encore and it runs off before you can do anything about it.
There's a big difference between Wobbuffet and Dugtrio. Dugtrio, first off, doesn't trap ANYTHING AND EVERYTHING. There's almost always at least one pokemon on the opposing team it can't trap, if not two or three. Dugtrio is also purely offensive. If it doesn't kill, it's probably dead that turn. Wobbuffet can take a hit, counter it back for a probable OHKO, and unless it was something exceptionally strong like Metagross or CB 'mence he'll be able to repeat that once or twice more. Since you can't switch, the only way to avoid getting owned is to use a non-attacking move which just gets you Encored and sets up free turns for their switch-in. You really can't discount these free turns; even if you have the otherwise optimum counter for a pokemon, CB Salamence eventually wears down a bulky water if it gets no time to recover health, T-Tar can do the same to Swampert, and so on, especially if they're using Spikes too. Once it's low on health or out of the way, or if you just don't have that pokemon in the first place, the Wobbuffet-user is set up for an easy sweep that you have almost no possibility of countering. Kinda like how Magneton screws you if Skarm is your only physical wall, except Wobbuffet acts like a mini-Mag for EVERYTHING. Most of the more common pokemon can wear down their "counters," so having said "counter" isn't a fool-proof solution to all the free turns Wobbuffet is giving to them.
Dugtrio can't do much but scavenge for kills on pokemon with low health or a weakness and low initial Defense/HP. It's basically removed from the team completely until you have an opening to get it in the game and steal a cheap kill, and most of that time that's just after you lose a pokemon yourself because Dugtrio's extremely fragile and has very few opportunities to actually switch in the middle of a turn. Wobbuffet, however, supplements the rest of your team, eliminating most heavy offensive threats (by, you know, killing it) plus giving you free turns for whatever the hell you want (Wish recovery, a Sub or Focus Punch, a DD or Swords Dance, a heavy CB blow). And quite the opposite of Dugtrio, there's very few things it CAN'T switch into and there aren't any pokemon immune to its trapping ability.
Plus there's just the fact Wob-Wob is absolutely retarded. When Dugtrios trap each other, it's over in one turn so there's no real inconvenience.