You should absolutely charge extra for hand-cutting if that labor isn't already built into your price, as it can take substantially more time and time is money! Aymee VanDyke has an excellent series on this site about cookie costing/pricing, which is a good place to get grounded in basic pricing concepts. You can find it here: http://cookieconnection.juliau...rom-dough-to-dollars
But in a nutshell, here's how you figure this out: time how much longer it takes to cut each shape vs. a regular cookie and come up with a total (extra) time per # cookies. Apply your labor rate and a markup to that cost to cover overhead and make a profit; then divide by the number of cookies for a per unit price.
So, for example, if it takes you 2 more minutes per cookie to hand-cut, and you have 60 to make, then that's another 2 hours of time. If your standard labor rate (what you pay yourself or others is $10/hr), then the bare minimum you would charge (with no markup for profit or to cover overhead) would be $20/60 cookies or $.33/cookie. But depending on your mark-up and overhead, you may want to charge even more - up to $.50/cookie or more would be reasonable depending on the complexity of the shape.
I think it only serves you to be candid about the costs associated with the extra time, or you will eventually burn yourself out working for nothing. This info also forces the decision about cookie shape into the hands of the consumer. I betcha they opt for a simple cookie shape once they know the time and cost involved. But maybe not - and then everyone's happy!