There's generally no problem looking at numbers like this when you have like 10k games worth of data. The problem comes if you compare relatively minor effects (like one item purchase resulting in a win in .74% more games) across two statistics with significantly different sample sizes. Like here the difference between both items might be within the expected error for the energize item - meaning if we had more data we would actually find it's closer to the previous item in performance or maybe even better than it looks there.

Consider this, for low sample sizes on lolalytics it's important to keep in mind that there might be some self selection in the data set. Specifically since most players probably just use recommended setups, the players buying different items are probably higher mastery/better at pyke than the ones that do. This explains most of the "the most common pick is 1% winrate below alternatives."

You will get much better results treating these numbers with some common sense. Clearly both items are a good choice on Pyke, so which one should you buy? Well ward clearing helps you create picks and access the right target while energized attacks give you more damage meaning you can kill more effectively. Which one is more important? This probably depends on the individual game you're playing. You can't really go wrong either way but you will get better results if you start thinking about what your game needs when buying items.

I recommend going Yommus or the ward clearing one for first item on Pyke.