Many horse owners who have fed flax in the past would gasp in horror at you if you asked if flax can be fed whole.
The fact is, flax seed CAN be fed as whole seeds. Recent research done on various seeds found that the nutrients were extracted from the seed hulls even if some seeds appeared "whole" in the manure.
Even though some whole seeds may appear in the manure, the majority of them are used completely in the equine digestive tract.
If you do decide to grind your flaxseed, make sure you grind it fresh for every meal. The nutrients start degrading as soon as they are touched by light and oxygen, so by the time you've ground them and dumped them in the feed pan, they have already lost nutrients. Ground flax can also go rancid very quickly. You can grind early and store extra in the freezer, which will prevent rancidity for a few days, but you are still going to have nutrient loss.
If you grind your flaxseed, also make sure you clean your grinder thoroughly after each grinding. Small pieces of flax can easily get stuck inside the grinder where they will quickly go rancid, potentially ruining future batches.