Yes. Some mods like kerbal engineer and machine everywhere makes thing less annoying, not easier. It’s the engines, fuel tanks, and science payloads that can break the balance.
As for mechjeb in particular, I never found it all that useful except when calculating rendezvous. I could do it myself, but I don’t want to bother with a protractor and calculator.
Mechjeb can help you with the boring parts. First couple dozen launches or orbital intercepts are super-fun. But once your goals shift from "let's land on the Mun" to "let's send a 250 ton ship to Duna", assembling it in orbit from a dozen launches starts to feel like a chore.
Mechjeb was far more useful/necessary 3-5 years ago. The stock game has added so many features at this point that I really didn't feel the need for any mods at all when I picked it up again a few weeks ago.
As for mechjeb in particular, I never found it all that useful except when calculating rendezvous. I could do it myself, but I don’t want to bother with a protractor and calculator.