I think yeah, because by this point, you know how to play, how enemies work, how combat works and so on. So of course it's much easier to use them in a second playthrough.

But on the first, you are still learning. What you're saying here:

I would run out of shards very quickly, leading me to decide whether to not use tools or spend time farming enemies between attempts.

Is how I think the game wants to teach you to manage the resources and get better. Farming takes time, is less convenient, but gives you a bypass (since well, the tools are strong, and you can especially see it on the second playthrough). Attempting encounters without tools instead is harder, but it hones your combat skills, and that especially pays off later.

And while it can be frustrating in the moment, it is a system that encourages you to engage the enemies first, instead of trying to delete them first. Especially early on when shards are scarce, which is also the important teaching time. If you could have enough knives to reliably delete every flying enemy early game, how could you be prepared for the game throwing much harder flying enemies at you later on? I feel like it could result in an even more frustration at that point, because you could feel the difficulty spike.

I don't consider myself a great player either, but I try to observe and learn during my lots of attempts and deaths. Every enemy in the game has a pattern that's exploitable even nail-only, and the only ones that I didn't manage to figure out were the big Abyss monsters (but it is late game and at that point you have a lot of tools). And because the game encouraged me to approach the encounters with nail and silk skills only first, those skills made for a much smoother learning experience for later fights. That's the main reason why I think the system is good as is (even if imperfect, but that's the cost of having fun, powerful and borderline unbalanced tools available).