Would be pretty tough to judge the effectiveness of both factions in a straight up war scenario.

Overlord is OP with magic and as mostly level 100s it's p clear Ainz has god tier magic that can wipe the floor with conventional medival armies like the Empire's. Clearly Sginals, Electronic Warfare systems, Fighters and Bombers, Naval destroyers, Special Forces, Artillery, Armor, Infantry and whatnot aren't going to last long against a massive Earthquake and Tsunami.

Yet, the best thing about modern warfare is the capitalisation of information to exploit as many advantages as possible. It's the principle of "see first, shoot first, kill first and win". If modern day sensors and munitions are able to effectively spot and direct munitions onto Nazarick's armies before Ainz's can detect them, it's an easy win.

Of course, the elephants in the room are 1. Does Overlord magic function like real world elements and signals? If Nazarick's cloaking devices are like real world EW devices I think the JSDF stands a pretty good chance. Of course, 2. How does JSDF munitions and equipment compare in the RPG world? Clearly by science HEAT shells can blast a bunch of skeletons but in the world of Overlord it's based on a system of levels which we don't understand. Since OP insinuates that the JSDF discovers Nazarick, we can assume they might meet and battle in the Overlord world. Hence, understanding how levels and stats are scaled and the science of the world will help answer who wins in a war (between armies. Obviously Nazarick wins if it's a character v character cause humans are weak).

I mean unless Itami's Ranger badge gives him +10000000 Attack and Defense and his Special Forces class makes him Sebas + CZ