I'm not super experienced with Sheik (only 75 or so with her), but this is my bnb setup for most characters. Massive wall of text warning, just read bolded things if you don't wanna read everything.
1) (4000 KOs) Hasty attacks: If it's not named young link, it wants hasty attacks. It boosts your speed to that of focus spirit. It might seem repetitive on Sheik, but it's hard to give up after you use it.
into your later combos faster. 2) (4000 KOs) Special Attack +: Sheik in particular has a fantastic special attack for AOE and damage, so capitalize on that. Finishing Blow + is acceptable if RNGesus hates you, but only if you're willing to spend the rupees to replace it with SA+ later.
3) (3000 KOs) No Healing: No Healing is amazing for a few reasons. First of all, you shouldn't be healing much anyways, so you might as well take the no drawbacks (if you're leveled appropriately) skill. The great thing is potions are now a semi-reliable source of special attack. Since they now only heal 1/4 heart, they allow for you to gain 4.5 bars of special back at nearly any time (the highest I've gotten to was 1.5 per drink, if it goes higher let me know). So bonus damage, more special spam... Probably the best 3000 KO skill, especially since water shield can soften almost every blow greatly. -Honorable mention to Compatriot, which is comparable to No Healing if you have 90% of the keeps. The problem is you're likely at the end of the stage if you have that many keeps, but the option is there if you still want to heal and don't care as much about A-ranking everything.
4) (2000 KOs) Vs. Dragon This covers two giant bosses, the four most annoying captains in the game (in my opinion), and Volga (since he breaks your guard a lot this is optimal too.) -Honorable mention to Vs. Beast for taking care of the other three non-dragon non-Ganon bosses. I like the bonus against the imprisoned since he's arguably the longest boss in the game, but the sheer amount of things Vs. Dragon boosts against is difficult to pass up.
Honestly from here, it depends entirely on the combos you use. Power up your favorite combos.
To answer your second question, Strong attack + only seems to boost fire and darkness to me, but lightning doesn't have much damage anyways, and water and light don't do damage from what I can tell. If you have the space and the skill though, there's no downside to having it. Just don't go out of your way to get it.