This is a reference to (or pun on) the idiom "on the half shell", which is a way of serving shellfish (but not turtles). For example:
on the half shell
of raw shellfish, served in the bottom shell, chilled and with condiments
—Dictionary.com
on the half shell
served raw, with seasonings, on a half shell
said of oysters, etc.
—Collins English Dictionary
It seems likely to me that the writer of the theme song identified this idiom with the old-fashioned practice of serving turtle soup in the turtle's shell. For example:
Accounts in the 18th and 19th centuries of massive parties known as “turtle frolics” suggest they were more popular than hog barbecues and oyster roasts, with descriptions of servants bearing three-foot-long upturned turtle shells filled with hot turtle stew for large crowds.
—Jack Hitt, What Ever Happened to Turtle Soup?, Saveur, 2015
Since Shredder often vowed to turn the Ninja Turtles into turtle soup, it seems likely to me that the two culinary references are related. While the idiom "on the half shell" is not applied to turtle cuisine in real life, turtle soup served in the upper part of the turtle's shell would indeed be "in a half shell" in literal terms. So, to me, the line is effectively winking at Shredder's failed threat that he would dine on soup made of his enemies.