Surely, you have to take a variety of factors into consideration...but I say, fix em!
I've used glue - and clear packing tape to good effect.
On MPC and LTI era boxes - just fix them! - They are so much stronger and more useful.
Pre-war flats - its up to you. Fortunately, glue works well on these.
One thing is for sure - LIONEL boxes suck! Made to be destroyed when used "normally"
Reverse the trucks and pray nothing catches!!!
And how do you open them without ripping the lids...I use a dentists pick to open some of them!