I don't think that is a problem at all. It depends on how much flow you are going to drop through those drains. Keep in mind that you have 2 primary and 2 emergency drains. Realistically, I doubt you will have a blockage in BOTH primaries at the same time. Also, the primaries don't tend to just stop dead suddenly, they are more likely to just block slightly, transferring only a portion of flow to the emergency drains.
Leave the emergency drains as straight pipes so you'll hear them if they become active.
Finally, just test it after. Block a drain and see what happens!
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400 gal reef. Established April, 2007. 3 Sequence Dart, RM12-4 skimmer, 2 x OM4Ways, Yellow Tang, Maroon Clown (pair), Blonde Naso Tang, Vlamingi Tang, Foxface Rabbit, Unicorn Tang, 2 Pakistani Butterflies and a few coral gobies
My Tank: http://www.canreef.com/vbulletin/showthread.php?t=28436
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