Eyestrain is a very subjective matter. What causes one eyestrain may not for the next. Best way to answer your question is to compare both first hand. It can certainly cause eyestrain for some and not others.
I have both devices here and the mini causes me eye strain. This is not only because of the smaller fonts! It is the screen that somehow makes everything too bright (compared to the Air).
This is the reason I am returning the Mini and keeping my Air. The quality of the screen is not that good. It uses old technology and has a lowr gamut. Now add to that the smaller fonts (because of the screen size) that cannot always be made bigger (apps have to support dynamic sizing in iOS).
I have tried the mini and for the reduction in size, I found it was not worth giving up the superior screen of the Air. I guess much is what you plan on doing with your device. Being a little larger is a plus for me.
I also prefer the colors and overall look of the Air.
I have been traveling with my rMini for several weeks--my last flight was about 15 hours, most of it either reading or watching movies on my rMini. I did not notice any eye strain. I also have an iPad 3 at home. Even at home, I tend towards using the rMini. But of course, it's a personal choice.
(I do wish iBooks had more gradual changes in the font size. The step sizes seem pretty major)
I played with a rMini at Best Buy and I thought the screen looked awesome. I did however zoom in because my eyesight is not the same when I was younger. Does that mean I won't get eye strain? I'll have to use it some and I have 30 days to return it to Best Buy, if I do.
So I don't discount those who have had issues with the smaller screen but there are many who have had no eye strain whatsoever. It's best to try the device for yourself and have a good return period in case you do have problems.
I have the retina mini, I had to bump up the size of the font but other than that, I can read everything just fine in landscape mode. No zooming to read something, and I am 40 years old.
If you want to read comic books, you can't increase the font size in the comics, and some comics wont let you zoom in so the mini isn't a good comic book reader (the air's bigger screen is better for comic books)
Other than that, it's good and if it's not, it's adjustable(other than comics). Remember everything is bigger in landscape mode. The mini is very light so its very comfortable holding it in landscape mode.
to be honest the regular iPad mini without causes a ton of eye strain for me, i can barely look at my gf's iPad mini for more then 10 minutes without my eyes hurting but with the retina display, nope never have, can look at it for hours and not a single problem
For me retina mini was fine when holding it close to my face, but as soon as I put it down for meetings or to watch a show, that's when my eyes would strain. I bring my iPad to all my meetings and prop it up using a Smart Cover with bt keyboard, and trying to read my notes I would get strains. Sometime enough to give me headache. After few days of use I returned it for an air and no more strains! I do miss the small form factor, I used it a lot more since it was so small.
I read on my rMini and I notice no eye strain. Obviously don't have the brightness all the way up; I think mine is about less than halfway. The lettering is not small at all, I could read it just fine - even when I wear my contacts. I don't notice any problems. I bought the rMini for the purpose of using it as a book reader and since I started using it, it's been perfect for me. Guess it just depends on the person.