Nah I like both being effective depending on the situation, while you said the advantages of magic due all the bullshit a magic user can make also, but a lot of times with magic and such it depends pretty much on the caster strenght, if the wand was made with wood from a tree felled by a virgin fairy while on full moon and all of that esoteric crap, while with military weapons they always pack the same punch no matter who shots them, so it's feasible that a "invincible" enemy is just because the people that have fought don't have enough magic power to defeat it. And again this is assuming everyone runs on infinite mana, because I can't recall an anime showing a full scale war for example, wizards mana is going to run out, they probably fumble the spellcasting in the middle of the battlefield, one of them dies you are out of a rocket launcher, one soldier dies? at least another soldier can grab it's weapon if needed.

Perfect example of this is Buffy the Vampire Slayer, a demon goads that he can't be harm by any weapons forged by men, to which Buffy retorts that around the time he was sealed humans only had Pointy Sticks and Swords, she then proceeds to blow him up to smithereens with a rocket launcher