This is a question that follows from article $4160$ of George Carr's book. He states that:
If $(x, y)$ be a point P in a circle $S$(where $S={(x-a)^2}+{(y-b)^2}-r^2$), then $S$ becomes minus the ordinate drawn through $P$ at right angles to the radius through $P$.
My doubt is :
By ordinate, does he mean the $y$-intercept of the line drawn perpendicular to the radius through $P$?

I think the word ordinate is used in an old sense related to conic sections. For example the Wordnik online dictionary gives one possible definition of 'ordinate'
In your document I think it simply means that if $P$ is inside the circle, the half chord through $P$ perpendicular to the radius has length squared equal to $-S$.
Note that $S$ is not the circle, it is the quantity $(x-a)^2+ (y-b)^2- r^2$. The result cited here is a trivial consequence of the Pythagorean theorem.