tl;dr: IVs and EVs are the same as they were originally while playing RBY. However, these values change when you transfer Pokémon to the Pokémon Bank. At this point, IVs will be semi-randomly generated upon transferral and EVs are simply set to 0.
The 3DS ports of Red/Blue/Yellow were kept virtually the same as the originals, even including the same glitches (like the Mew glitch on Nugget Bridge). For reference, here is a list of differences between the 3DS Virtual Console versions and the originals.
This means the old EV/IV system was also maintained. However, this does not translate to the current system, as you've mentioned in the question.
According to this article based on datamines of the games, it doesn't have a system similar to the current one at all. In fact, it seems that Pokémon will simply be assigned EVs and IVs when transferred to Pokémon Bank.
Individual Values (IVs) are determined randomly. However, at least three stats will have a perfect value of 31. That means that every transferred Pokémon from RBY will have three good stats at least! The exception is Mew, who gets at least five perfect IVs instead.
Effort Values (EVs) are set to zero.
Similarly, Natures will be generated upon transferral, though these are based upon EXP earned.
Nature is an interesting aspect. Bank determines what the new Nature is based on the gained EXP of the Pokémon:
Nature = EXP % 25
% represents the ‘modulo’ operator, and gives you the remainder when dividing by the number following it. If EXP was, say “1001”, the equation becomes 1001 % 25 = 1, as dividing 1001 by 25 gives you a remainder of 1.
Each number corresponds to a Nature, which is listed below (assuming the same system is maintained). If you’re determined to get a good nature for your RBY Pokémon, you can give it some EXP to do just that!
![Nature chart](https://i.stack.imgur.com/xiigq.jpg)
As for Abilities, most Pokémon appear to be given their Hidden Abilities, with the exceptions being those that don't have Hidden Abilities:
Almost every Pokémon from RBY will gain its Hidden Ability. There are three exceptions; Mew, the Weezing line, and the Gengar line. This is because these Pokémon have no Hidden Ability.
This means that Machop will not have the No Guard Ability when transferred. No Guard Fissure Machamp can’t exist!
Best Answer
Credit to Crystal_ @ forums.glitchcity.info
Quoted from the source:
All of these make sense -- it's how the game works. But here's the catch : the "PP increment" function doesn't check for the Transformed status !
Here's how to trigger the glitch :
Thus, the game increments a move's PP in the Pokémon's data. If the move is present, then it will just have incremented it, no biggie.
If it's not, this creates a slot that is empty, but with non-zero PP ! Thus, the game fails to use Struggle.
Disable
Disable first checks if there is a slot with non-zero PP, and if this fails, misses. With a Struggle-less Pokémon, this will always succeed, because of the glitched slot. Then, Disable will attempt to pick a slot which must have a move AND non-zero PP. Assuming Transform has 0 PP, the game will never find such a slot (since the only slot with non-zero PP has no move). Bam, infinite loop, and softlock.