By the time electromagnetic signal gets pinged back to your ship the enemy will be in totally different place.
By the time the human operator sees the enemy on the monitor the enemy will be in a completely different place. A light-second is not a big distance in space, so it's impossible to ever tell exactly where anything is at the present moment.
And regardless, the human operator would still have to use an IFF, because there's no other way to know what they're looking at. That means firing an electromagnetic signal and waiting for a response. Same thing, just slower.
And we all know, just from looking at a picture, that we see a ship.
When you see pictures of distant objects taken in space, they are taken through incredibly powerful telescopes. Those telescopes are not only very, very big, but they can only look at a tiny proportion of the sky at once. They also take a long time to set up. If you think it's going to take a long time to use an IFF, then how long do you think it's going to take to rotate and set up your massive telescope to look at an object hundreds of thousands of kilometers away?
Since you can't realistically install a massive telescope on your spaceship, and you certainly can't expect to be able to use it, what you have is a very basic electromagnetic transmitter and receiver, like a radar system, which means you don't see a picture, you just see a blip, and that is all you have to go on.
Also, is space really empty?
Yes. Space is extremely, incredibly, unimaginably empty.
You could be in the middle of the asteroid belt, and the entire diameter of earth's atmosphere would likely not cover the distance between you and the nearest object capable of appearing on your radar. Space is really, really, really empty.
Not to mention that IFF signal might be copied and it will render your entire fleet useless.
Maybe. However, if your spacecraft were manned you'd lose your entire fleet and all the humans crewing them. You've wasted millions of gallons of fuel launching all this completely useless life support into orbit just to have a human there who.. could do nothing, and died.
At the kind of distances we are talking, human operators would be completely and utterly at the mercy of their equipment. They would have absolutely no ability to discern what was going on except by looking at blips on a screen. A computer could do the same thing only faster, and without requiring many tons of additional equipment.
It's clear you really like the idea of manned space warfare and I can respect that, it makes for more interesting and fun science fiction, but barring some technological singularity beyond which the future becomes impossible to predict it will not be realistic. Space is very big, it's very difficult to take anything there and it's very dangerous for living things to be there, so even if a human operator did confer an advantage (which I really can't see how it possibly would) it would have to be an advantage capable of outweighing the huge costs and design challenges of putting humans in space in the first place.