I just leave them on, out of pure laziness… but I have a few times gotten a bit of contaminants on there since they move about a bit in the wheel bags, and there is grease on the hub ends etc.
Nothing that isn’t easily solved with some disc brake cleaner, but either way, been fine so far with like 14 flights.
I have one of the compact, soft bags. Take the rotors off for three reasons:
Theyll pack better as the wheel’s hubs “tent pole” the covers; the disc expands this area.
The discs are thin and bend. A slight bend equals noise.
Oil can get on the discs and cause issues.
The tools are pretty light and removing them is easy. There are two styles - centerlock and 6-bolt. The 6-bolt (mostly MTB wheels), you just need a metric hex / allen wrench that you probably already have. The Centerlock uses the cassette lockring tool…
I take rotors off. It’s a 30 second job and I’m twitchy about them getting dinged by something in transit and then rubbing. I also tend to carry lube in my BBA so want to avoid any potential contamination, unlikely but again easily avoidable by just packing the rotors away.
I take them off, wrap them up (CLEAN rag/bubble mailer) and place/tape them in the bottom of the case. I have a soft side case that has a rigid bottom where the frame/fork rests. that seems to be the best place to protect them from any impact/damage.
Take them off and use manila or padded mailing envelopes to keep the discs in.
Also, get the correct block to put in your caliper to prevent grabbing the levers and maybe needing a bleed.
I have a left-over protector for the disc brake rotors which slots into the quickrelease hole. It is just a plastic disc with a pin, and the diameter of the plastic disc is larger than that of the rotor. Card board should work fine, too.
I have taken my bike on many long-distance trips (Europe-Canada and Europe-Japan), and never taken my rotors off. I wouldn’t do that, otherwise you’d have to align them.
About the rotors in particular? Apart from the protectors, no.
Here’s what I did and it has worked for me: I have asked local bike shops for empty bike (cardboard) boxes. I took my front wheel, seat post and handlebar off. I put bubble wrap round my handlebars, my top tube and affixed my handle bars on top of the top tube (protected by bubble wrap). I also bubble wrapped the seat post and taped it around the bubble wrapped seat tube. I used towels and bike clothes to pad the box. I put the front wheel in between the box and the mid-section triangle of the frame. I put the wheel on the right side to protect my rear derailleur. I made sure that wheel and frame were padded. Then I added more towels and padding. I always made use of the 23 kg weight limit.
If you have a bike case, then it depends on the case. Some cases are bare bones inside (mine is). Others have very elaborate interiors where you put your frame on a platform, you have wheel bags, etc. But in any case, I’d err on adding too much padding. Some baggage handlers are rough.