how good are protein flapjacks compared to shakes?

Well assuming that you buy equal quality products with the same protein content then there isn't a massive difference between the two... As already mentioned protein bars can take slightly longer to be absorbed and therefore you may not get the full protein benefit but you could simply eat the bar a little before the end of your workout. A major difference is value for money, you tend to get a lot more for your money with shakes but then bars have more portability if you're out and about without a shaker.

I like to have both but I make my own protein bars/flapjacks with shake powder, that way I get the value, portability and I can control what goes in my bar!

Powders can be more quickly absorbed by the body although they don't taste as nice.

Protein bars usually carry a high saturated fat, sugar and/or high sodium content - not exactly ideal for general health and reaching results.

This might not make a huge difference to you, but they work out to be more expensive as well.