NPApe is going to be extremely dangerous with Nasty Plot/Fire Blast/Focus Blast/Vacuum Wave. Pretty much the only counters for this set are Tentacruel, Defensive Starmie, Bulky Gyarados and Cresselia, yet, with the exception of Tentacruel, they all have the chance of being OHKOed after SR and a NP. Vacuum Wave is mainly for ScarfTar but considering it will probably decrease in usage due to to absence of Latias, Grass Knot will be a better option as it allows me to OHKO Bulky Gyarados and Defensive Starmie, leaving just Tentacruel and Cresselia as counters. Tentacruel can be trapped and OHKOed by Dugtrio while Cresselia can be worn down by Pursuit from the likes of Tyranitar.
And that's the reason why banning will help alot in metagames creativity It always happens with major bans. Someone remember what happened after Garchomp ban ? There was time were Nidoqueen started to be popular because she was almost perfect Lucario (and more popular back then) Heracross counter. Also stuff like Salamence and Flygon started to show up. It helped alot in finding new pokemon to use and make metagame more interesting. Here we'll have similar situation.
NPApe is dangerous, but as you said counterable. And heck, some of Apes counters are in... UU. Thick Fat Grumpig & Hariyama and Slowking are examples of this and they may provide you with little unique niche. You just need to lurk more if something is gone. I remember I used in one the stall teams before Latias era specially defensive Dusknoir and it worked really fine being good rapid spin blocker for Starmie and it was my really good Infernape check, as it couldn't OHKO me back and I would do it in return. Cresselia, Mesprit and Uxie may still do the same if EVed right. Vaporeon survives every nasty plotted hit from Infernape except Focus Blast. Situation is identical with Lanturn, which is really light, so it laughs on NP Grass Knot and Lanturn is perfect Starmie check, which may rise now alot after Latias ban. Bulky waters and Ape check in one ? Yes please. ANother interesting example is Dragonite, which check standard NPApe.
About Tentacruel - if you face this SDApe... so what ? Swampert is part of stall teams and he checks SDApe really well. I may say the same about Hippowdon, Donphan, Slowbro (yes, it survives SD Life Orb ThunderPunch), Suicune also survives SD ThunderPunch from SDApe and even... Thick Fat Hariyama (again, but this time physically bulky). And rarely SDApes carry Mach Punch, so ScarfTar may still check it to some extent. Or ScarfRachi with Zen Heabutt or ScarfTran with Earth Power (and I used both on my semi-stall or stall teams). Really, there was time when NPApe and/or SDApe were free from Latias and metagame somehow easily dealt with them. Infernape usage will go up, but it won't change much and stall teams still have their ways to deal with out fire monkey. And Infernape is quit frail, so Infernape users have few problems before using Apes power to maximum.
And why I mention those UU/NU pokemon ? Because they weren't viable before, but NOW they may be. Just to say Hariyama again and not to make it outclassed by Machamp ? Hariyama is perfect Tyranitar counter and unlike Machamp Hariyama may handle Infernape thanks to fire resistance. Heck, Hariyama may check Scizor (if you carry Fire Punch) and take those CB U-Turns all day long with Wish support. And unlike Machamp Hariyama may phaze thanks to Whirlwind. Now I seriously consider Hariyama for stall team as earlier I would hate to use it because it gives Latias free switch. We know how dangerous it was.
And yes, I'm happy with Latias ban as it gives back this creativity which metagames missed after her OU entrance. Also her unpredictibility forced me to some serious specializations, making it just less enjoyable. I honestly don't think that Latias was unstoppable, however it was extremely hard to do it if someone used her right.
Man all this theronymon about other pokemon being viable (UUs) makes me think that some ppl haven't played pre-OU-Latias era, I did (though honestly not much) and no actual UU was used back then to counter Ape, just your average Tentacruel/Gyarados/Vaporeon (this one is a little unreliable now because of the "discovered viability" of focus blast) and that was pretty much it.
I played and yes, you're right that they weren't used. But it doesn't mean you can't use them and still use them in COMPETITIVE way. Sometimes you just need to lurk more to discover something interesting. It took a while for example for Smeargle to be OU and I may the same thing about Tentacruel, which at early D/P was almost non-existant. Maybe my Hariyama mention will help it, as it is much better pokemon then people think.