What are the advantages and disadvantages of developing OpenCV applications in Linux vs Windows?
Linux solutions would be distributed for Linux systems.
And Windows solutions would be distributed for Windows systems.
That's all.
OpenCV is cross platform, so it doesn't matter what is the targeted system.
As for IDE, again, it doesn't matter. Use whatever you're using now (or see http://www.cplusplus.com/articles/chrisname1/ ). IDE is not in any way related to libraries you use.