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Not quite, while in principal they are the same, the 18650s have always gotten the most attention and development from manufacturers.
The capacity specified in mAH is generally used to estimate runtime. Using two 16340 in series means runtime is still based on 650mAH but driving something @ 7.4V as opposed to using one 18650 rated at 3000mAH driving something else @ 3.7V . That is, the 18650 will 'run' roughly 4.5x longer than two 16340s.
Are you sure about that two 16340 batteries gives more output power because of 7.4 V?Not grave digging but just so other noobs like me know, 2x 16340 will produce 7.4V compared to 3.7V of 1x 18650. This can be a major factor when it come to powering the laser. The 18560 will yield much longer life however since it generally has much higher mAH i.e. 16340 = 650mAH and 18560 = 3000mAH