Annualised hours is when you work more hours during certain period of the year and less hours during other periods.
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This sometimes happens when it's not the individual hours, but the period of time that's being referred to. As a period of time, 100 hours is less than 200 hours. While it's true that 100 hours are also fewer than 200 hours, the sense here is of two blocks of time - hence both 'less' and 'is'.
Here's another example:
A: "I walked for 10 miles yesterday."
B: "That's nothing. I walked for 20 miles, so you walked less miles than me." (This is probably substandard, but you'll hear it a lot.) The point is that it is the distance that is being compared. "You walked a lesser distance than I did."