The name MacKendrick/McKendrick/M'Kendrick/Kendrick/McHenry/McHenryson and a few other variations are all anglicized variations of 'maceanruig' the gaelic for 'Son of Henry'. Henderson is the most common variation of this anglicized surname. Since there were more than a few 'Sons of Henry' in Scotland you will find the surname Henderson is borne by numerous unrelated families in Scotland.
However since your ancestor was (possibly) a McKendrick it's most likely they originated from the sept of Clan Donald that lived at Glencoe prior to the Massacre at Glencoe. At least this is what is commonly cited in written histories and this has been part of my family's lore going back to my great-great-great grandfather and his brother.
Now, as to why they would change the name - if you visit the Wikipedia page on Henderson http://en.wikipedia.org/wiki/Henderson_(surname
) you'll see that the author claims the surname was 'unknown in England before the 17th century.' What was happening after that to make it less desirable to have a Scottish name? Assimilation and persecution, basically. I'm still researching why there are so many McKendricks in Antrim suddenly in the 17th century, but here is an interesting read if you're inclined. http://www.ulsterheritage.com/scotsirish/s_i_history.htm
Note the part about the 'Campbell/MacDonald feud and then Google the Glencoe Massacre.
To sum up It is basically, an attempt to fit in by making a very foreign (Scottish) sounding name more English. So one theory is that your ancestors decided they would be more comfortable in the melting pot if they had the English form of McKendrick. There is no set rule about how to anglicize the name, but Henderson was and still is by far the most common form so that's probably how the decision was made.