Yes a motherboard can crack under the weight of a CPU cooler but most have a CPU backplate that helps support the cooler to prevent cracking. As long as you have the backplate installed you shouldn't have any problems with cracking.
Yeah this is the thing that has me saving up for a Corsair H100 right now. I originally wanted to get something like a D14 but man those things are freaking huge!!! Im pretty sure it wont crack my beloved Sabertooth, but man I dont want to take the chance. Plus I dont like my CPU cooler eating up half my RAM slots either. My Hyper does that now so I can only imagine what a monster heatsink would do. Yessir, its H100 or possibly a Kuhler 920 for me.
All in one water cooling kits are IMO not that great. You look at the test done and in the end they don't perform any better than high-end air coolers like the D14. Sometimes they don't even perform as good as high-end air cooling depending on the brand and model of the kit. I would go with a high-end air cooler like the Noctua D14 or if you really want to do water cooling do a custom water loop. To me those all in one kits are a waste of money.
Yeah they can be cause ones like the H100 are $115-120 where a D14 can be had for around $80 I think. The H100 does perform a little better than the D14 but only by 1-3 degrees depending on which website youre reading.
I guess it really comes down to if its worth the extra $30 to save the space inside your case and not have to deal with a super massive heatsink. To me, it kinda is cause as much as I like to upgrade stuff, it would be nice to just reach in and pop out my RAM with no problem.