No, as I wrote above all the sticks will be used. Memory access to that last 4 GB will be slower than memory access to the other 8 GB.
1) Unless you really need more than 8 GB, if I were in your shoes I'd only use two modules.
2) Are any two modules in that set from a matched pair? Since the advent of dual-channel memory, vendors have been selling memory modules in matched pairs that have been tested together. It's better to use the two that are a matched pair.
Different people will have had different experiences and tell you that using unmatched memory makes no difference, slows your system down noticeable, or makes your system die. It depends on what experiences they had.
So if you need fastest memory performance, use two, preferably two that came together. If the extra memory is important to you, either use three or go buy a matched pair and use four. Or just buy one more and see how four totally memory modules work together.
EDIT: Depending on the motherboard, with three sticks it will either run single-channel or dual for two sticks and single for the third. See this thread:
http://www.tomshardware.com/answers/id-2096208/pros-cons-sticks-ram-dual-channel-motherboard.html and Tradesman1's answer.