If 0.99 inch is 1 inch shy, how to call 1.01 inch?
Just over an inch.
I would pronounce that "One point oh one" inch
If 0.99 inch is 1 inch shy, 1.01 inch is over one inch. This is because it has a .01, which makes its more than one.
No one would say this. You don't measure inches in decimals. Both of those would just be called an inch. Also the expression is ".1 shy of an inch". The way you have it doesn't make too much sense....
How accurate do you want to state the measurement? You can go from "a speck over an inch" to actually giving the true measurement - in any number of formats - it all depends on the needed accuracy you want to convey.