Lord Krishna and also Lord Shiva are often depicted deep blue in color. This theory was also copied by James Cameron in the movie avatar.
The spiritual fact for this deep blue color existed in the underlying principle of spirituality.
Every single moment of life human beings invoked both positive and negative thoughts. The churning of these thoughts spiritually is called Samudra Manthan. This churning resulted in production of Amrita (elixir of life) and also Vish (poison). Precipitation of positive thoughts resulted in production of Amrita and those of negative thoughts in Vish.
By channelizing Amrita human beings finally succeeded awakening their kundalini shakti fully right up to crown chakra (also called Ajna chakra). The Vish could either be retained in the body, in the neck or gulped out. This is purely depended upon the spiritual capability of the individual.
Lord Shiva retained the Vish in the neck hence his neck is always shown dark blue in color. If the Vish (poison) spreads to body it is shown dark blue in color. No matter how best a self realized soul tries, some of the Vish percolates to the body resulting in dark blue color.
In case of Kalki Avatar the case would be both. He would also succeed gulping out most of the Vish but some of it inadvertently would retain in the body. Not necessarily the body of Kalki Avatar would be dark blue in color. The most that could happen was death of Kalki Avatar by throat cancer. Similar was the case with Sri Ramakrishna Paramhansa who died of throat cancer.