Most field offices hold oath ceremonies with name changes just fine during the pandemic while courts are closed, but as you experienced not all do.
I would advice against getting a new naturalization certificate unless you really want one in your new name and want to spend the extra money. Once you receive your passport (that you apply for with your current certificate and name change document from court), and update your info with SSA (and possibly DMV), you will likely never use the certificate for anything ever in your life. Sure it can happen, but it's unlikely. For citizenship and ID you use your passport, which will have your new name. So is it worth it to spend all that money on something that will just collect dust among other documents? That's up to you. I know I wouldn't have done it.
I think you're doing the right thing getting rid of names that just cause trouble in the US system, it does make life easier. Where I'm from almost everyone has two "middle names". Two middle names are really an annoyance here in the US, especially if they're long, and they caused me issues on both i-94, my SS card and at DMV, banks etc. So during my naturalization process I got rid of one of them, now I just have First Middle Last. So much better. It may be more work for you, but if you plan on living the rest of your life in the US you're doing yourself a big favor.