No your orbit will not decay as long as you are above the atmosphere, even if your orbit dips into the atmosphere your orbit will not decay if you are on rails. Your orbit will only `wobble` when you are controlling your craft and not on rails.
Unfortunately if you have not got another save and you did not quit immediately (using ALT-F4 or the task manager not the normal menu) when you got the warning message then yes, all your craft are gone permanently.
It will not help your current situation but I use the mod `mechjeb and engineer for all` which gives you the function of mechjeb and engineer in all your pods and probe cores so you do not need to add the MJ part to your craft.
For the future also you may wish to try Jebretary, a Git based version tool which backs up every save, quicksave and craft you make and you can go back through all the versions and restore whichever one you choose. There are other mods which have this function but this one works well and can be controlled through a web browser.
EDIT : Next time you get that message, quit straight away using ALT-F4 or go to windows and close KSP. Don`t go through the menu as that will save your game making all changes permanent.
John FX's post in Wobbling Orbits was marked as the answer