Will using Javascript sorcery have a negative effect on the game?

I found a possible side effect. If you eat a ridiculous amount of candies, your hitpoints will get so high, that...

...fighting yourself will take a long time:

No

I needed to sleep, so set candies.candiesPerSecond very very high so I could complete the game and get to bed.

There are no negative side effects, I was even able to save and reload the game.

Since javascript has dynamic variables, you can make the numbers as high as you possibly want as long as javascript can handle it. For AFAIK there shouldn't be a problem with huge numbers. It will be transformed to the e-notation. Once you finish the game and randomize everything using the "computer" it also comes up with such huge values.