You can use Strength Sap, Shiinotic's signature move, to check Nihilego's Attack stat ([Attack]=[HP pre-SS]-[HP post-SS]) before catching it and a Pokemon with a specific speed (preferably a Dark type) to know whether Nihilego's speed is larger/equal to or lower/equal to a specific number. Here's the three main ways they can be used for SR'ing:
Variation 1 - Always Timid, but tosses some Timid ones:
Overview: By using Strength Sap, you can check to see if the Nihilego's attack is 62 or lower, and you can use a Pokemon with 136 Speed to check if Nihilego's speed is 136 or higher. If its attack is 62 or lower or its speed is 136 or higher, then it's Timid nature.
Set-up: Use a Fainted Timid Synch in Slot 1. Have the Strength Sap user in slot 2, full recommended moveset Spore, Strength Sap, Substitute, Confide. High HP investment is recommended for it, at least make it so Substitutes bring the Strength Sap user down to Max HP-63. In one of the four remaining slots, put your Pokemon with 136 Speed, Moves doesn't really matter for it, but if you can give it False swipe, that would be good.
Checking Process: Turn 1: use spore, if Nihilego didn't bring you down to a point where an acceptable Strength Sap doesn't fully heal you, use substitute, then use Strength Sap. If the Nihilego has 62 attack or lower, switch into your speed check and use a move like False swipe or such. If the Nihilego doesn't outspeed you, you could either toss or try once or twice more to make sure it's not Timid. If the Nihilego did have 62 or lower attack and did outspeed your checker, then it's Timid nature and should be caught to have its Hidden Power type checked.
Pros: Makes sure you won't waste much time on non-timid Nihilego.
Cons: you could theoretically toss really good timid spreads.
Variation 2 - Toss a bunch of non-timid ones, but still has a chance to catch non-timid ones:
Pretty much the same as variation 1, except only SR over the Nihilego, if its attack is 73 or higher or the Speed is 128 or lower.
Pros: Gives you a higher chance of the Nihilego's you check having a Timid nature
Cons: Still gives you a chance that you'll even check and check something like a an Adamant 31/2/21/27/31/31 Nihilego.
Variation 3 - 0-1 Attack
Overview: The variation I did. I recommend not checking speed here, since that's so insignificant and unreliable in comparison to checking attack, though something like a speed check of 126-127 speed wouldn't hurt, especially if that's a dark type that's also your false swiper. In this variation, you'd check if the attack stat is 56, because if it's higher than that, its attack IV is 2+, meaning it'll take more damage from Foul Play and such.
Set-up: Synch and strength Sap user is the same, except you'd only need the strength Sapper's HP to get down to user's HP-57 after a sub, and as mentioned earlier: you don't really need a speed test.
Checking Process: also pretty much the same as variation 1, except for the attack number being changed and speed check not being that necessary.
Pros: The Nihilego will end up with 0-1 Attack, meaning it'll take minimal damage from foul play and confusion and be perfect after Hyper Training
Cons: Much lower odds than if you just go for Nature and Hidden Power.
Note: Dark types are preferred for Speed checks, because Nihilego can screw up Speed checks by using Mirror Coat. However, it won't use that if a Dark type is out on the field.
BTW, Sorry, I know this is a "ask a Simple Question, get a Simple Answer" thread, but I really wanted to go this deeply into explaining one of my favorite moves.