Once you reach 5000, and upgrade you are done, and legally can make as much money as you want. If you don't upgrade and make money over and above the 5000 then nothing will happen, BUT if you start making decent money and scirra gets wiff of it - you will end up in a lot of trouble and legally you will loose. Best upgrade when you need too, and enjoy all your hard earned money.
Nothing changes with your game, its the same software, its just the right to make profits from your game that changes. Same apply's to other softwares / unity etc who offer x amount of profits before requirement of licenses.
I know it is tempting to fly under the radar once exceeding the stated amounts - but it isn't worth it in the long run.
Give to Caesar what belongs to Caesar so to speak :)