Thanks. Mods sometimes become the antagonists, so I'm glad there are people who don't feel that way about me :p
Re Empoleon EVs: I guess the question you should be asking is *why* you want Def and SpD to be equal to begin with. You want EVs spreads to boost your most important stats (obviously) and to give you tangible advantages in common matchups (e.g. running extra speed to hit a benchmark, or extra HP to survive an OHKO). Does the EV spread achieve something like that, or are the stats balanced 'just because'?
To answer more succinctly: it might happen by coincidence that you run an EV spread that makes Def and SpD equal, but it's not something you should set out to achieve.
Re usage stats: You can't always discern checks from counters by looking at the stats only -- but the Pokemon that perform well in those listings are more often counters than checks. The data tells you how often each the Pokemon KOs the main Pokemon you’re looking at, and how often they force it to switch at any point (hopefully that answers your second question?). The percentages are then combined and weighted to give a measure of 'confidence' about that Pokemon's performance in the matchup. (That's the number that appears beside the Pokemon's name.)
A Pokemon that counters another is going to KO it or force it to switch in more situations than one that merely checks it, so you'll generally see counters in those stats. Note that the stats don't necessarily tell you the *best* way to counter the Pokemon -- they're just figures that tell you how the recorded matchups played out, for what it's worth. Exeggutor is listed as the #1 Rotom-W counter in the page you linked; and as much as Exeggutor probably does counter Rotom-W, I can guarantee that listing only looks the way it does because of low sample size. Exeggutor is not a good Pokemon in UU overall.
In short, the stats are useful to give you some pointers about what happens in the metagame, but you can't treat them as absolute, and you need to gain your own experience to put them in context. One way to trim the fat is to look at the stats for higher-rated games, so the random mon that Jeremy took into the lower ladder doesn't distort your perception. This page for 1500+ Elo rates Roserade as the top Rotom-W counter in UU, which is a bit closer to the truth (
https://www.smogon.com/stats/2020-08/moveset/gen8uu-1500.txt). Just remember that there is less data for high-rated games, so the list of counters might thin out if you go to the 1760+ page.
This ended up quite the tangent -- hopefully it all makes sense!
Re guess answers: If you don’t know what you’re talking about, then you’re probably just guessing. If you’ve got some experience or found something on the internet that gives you an informed opinion, then you’re not guessing anymore (but you still might not always be right).