Lets take a more detailed look at what Wynaut could outspeed and Encore in OU.
OU Pokemon that Wynaut can outspeed / how many Speed EVs they need to avoid this:
Pokemon who often (by the latest stats) run a non offensive move and are viable targets are underlined.
Tyranitar / 8
Dragon Dance is on 36%, but those run plenty of Speed for Encore to not be an issue (and Crunch is going to blow Wynaut away). LeadTar could have some problems, but 8 EVs is tiny. Boah is outsped, and could have problems if Wynaut comes in on a Substitute, but switching a Psychic type with 48 base Def into Tyranitar is an insane prediction.
Magnezone / 16
45% of Magnezone run Substitute, they run 84 Speed anyway.
Swampert / 16
70% of Swampert run SR and few have speed, but only a minor EV change is required to avoid this problem. Dropping 4 points from HP or Def will rarely make a difference.
Empoleon / 16
45% of Empoleon run Substitute and 23% run SR, but a vast majority use more than 16 Speed already.
Blissey / 56
Blissey would likely be the most common target of this strategy (unless it invests in Speed) as it has low offensive power and often uses non threatening moves. Thunder Wave or Toxic would cause Wynaut annoyance at least, but it should normally be able to Tickle Blissey 6 times or stall it out of Softboiled PP. 56 EVs is a noticeable loss, but only 14 points which would cause less than a 4% drop in its ability to take Special hits if taken from SpD. Compare that to over 40% of Skarmory declining 6% recovery per turn to avoid Magnezone death, and it seems insignificant.
Machamp / 16
27% of Machamp run Substitute. Others have some problems, but even with the resist Wy takes 38.3% - 45.2% from DynamicPunch (without CB) and there is confusion on your side.
-Speed Swampert / 80
Relaxed MixPert does have a problem with Wynaut, but if it uses EQ rather than SR it will deal a hefty 50% - 59% and can force Wynaut into a prediction war with Ice Beam (which deals 24.1% - 28.6%, so two EQs and an Ice Beam either KO or leave Wynaut as death fodder).
Hippowdon / 120
Another Pokemon that has problems with Wynaut, but again its Earthquake deals a solid chunk of damage (50.6% - 59.6%), so Wynaut is not going to be happy if it comes into the wrong move. Still a decent target.
Dusknoir / 136
Would be a great target if it was not for:
| Dusknoir | Move | Shadow Sneak | 47.1 |
and the fact that it is immune to Counter. A Wynaut switching into Duskull has a high chance of either being able to do nothing thanks to Shadow Sneak (other than encore a STAB SE move) or coming onto an offensive move it can't even Counter. The best that could be hoped for would be to waste Pain Split or W-o-W PP.
Bronzong can't outspeed with just an EV change.
Wynaut would love switching in on the screens or SR from Bronzong, but the chance of Hypnosis, Trick Room, Trick (with an "always go last" item), or Explosion make it risky. Can trap and Counter to death Bronzong Encored into EQ/Gyro Ball.
Forretress can't outspeed with just an EV change.
Another prime target for Wynaut, any move but Explosion will give Wynaut a free run. However, if Encored into using a multi layer type of Spikes it will be fully laid which somewhat compensates the player who lost Forry. Also, 27% already run Shed Shell for Magnezone which could let a player get 3 layers up, then switch out for free!
Snorlax
Snorlax can do solid damage with it's STAB attacks:
Body Slam: 42.5% - 50% with no Atk, 86.7% - 102.1% with max Atk and CB
Return: 50.9% - 59.9% with no Atk, 103.9% - 122.3% with max Atk and CB
Curse/Rest Snorlax (just over 50%) would have major trouble if Wynaut comes in on the right move.
Also, for comparison since there was some testing done in UU here is a list of UU Pokemon that Wynaut can outspeed: Clefable, Weezing, Torterra, Omastar, Aggron, Azumarill, Chansey, Donphan, Hariyama, Regirock, Registeel, Tangrowth, Rhyperior, Spiritomb, Slowbro, Steelix.
There are a significant number of Pokemon who the Encore/Trap combo could be effective against, however against almost all of them it is far from risk free. It can still do the same thing as Wobbuffet, but to far fewer Pokemon (No Speed Breloom, Metagross, Skarmory, Scizor, and Vaporeon sit between 159 and 181, and the rest have to invest 88 less EVs in order to outspeed it) and importantly with much greater risk. Yes Wynaut is not going to be 1KOed by much, but it can't shake off STAB attacks and Counter/MC back comfortably if it comes into the wrong move. Every Pokemon above other than Blissey who would usually use a non offensive move (and so be a target for Encore) can either deal 50% or more damage, get a free full set of Spikes/Toxic Spikes, threaten with Explosion, or use frustrating non direct offence move.
It's worth noting that freely removing Pokemon, or blocking the option to escape, under specific conditions is nothing new, Dugtrio, Magnezone and the Pursuiters (most notably Tyranitar) can all KO Pokemon which the owner would like very much to switch out. Those tend to do better against frail Pokemon, those with weaknesses to Ground, Electric, or Dark respectively, or those at low health. Wynaut (with the Encore/Shadow Tag combo at least) would seem likely to do better against very slow Pokemon using a move which does no damage.
Edit: and Bologo said much of this while I wrote/ate. Should've refreshed to check for new posts.