Well Kakashi did not use his Kamui too often until the 4th World War.
I remember him using it against Deidara, Pein and to dispose a Susano´o arrow from Sasuke (did I forgot anything?).
Thats not too much strain to the eye.
And even in this war, how often did he use it? Maybe 4 times against Obito? Still not THAT much.
We have to remember that it depends on the technique very much, for example it looks like casting Amaterasu damages the eye alot more than Tsukuyomi. (Looking at Itachi, his eye always bleeded while using Amaterasu but not while using Tsukuyomi).
Amaterasu is nearly a pure offensive move and it creates flames from the eye, that really is something, Tsukuyomi however is "just" a Genjutsu, nothing gets created from the eye.
Kamui seems to be smiliar to Tsukuyomi, nothing gets created from the eye either, its the complete opposite the eye consumes the target into another dimension. It could be that this technique is also pretty nice to the eye..lol.
However Kakashi did admit that his eyesight is getting worse, at the first meeting with Itachi after the timeskip he asked Itachi "Itachi, how bad has your eyesight gotten?", theres only one way for Kakashi to know that the eyesight gets worse after activating the MS, experiencing it himself.
