If you only think of Booleans as 0 and 1, then it is natural to include them as subtypes of natural numbers and integers. But as soon as you start applying operations to them, then things start to fall apart.
Consider what happens when you define the + operation on Booleans. You have two choices:
Make + the same as OR, so 1+1=1. But then you have the problem that + on Booleans is no longer the same as + on Integers, which it should be. More precisely, we have the following $(Integer)1_{Bool}+ (Integer)1_{Bool}\neq (Integer)(1_{Bool}+1_{Bool})$, where $1_{Bool}$ is true and $(Integer)\_$ is performing a cast from Bools to Integers. This means that there is a problem with coherence in the subtyping relation is we make this choice.
The second choice is to define + on Booleans so that 1+1=2. But now the operation takes you out of the world of Booleans. Semantically, this is not problematic ($\sqrt{-1}$ takes you out of the world of Real numbers), but it does suggest that you do not gain much by treating Booleans as numbers.
Generally, the way Booleans/Integers are treated in languages like C is that Integers can be used in places where Booleans are expected, which does not really follow the usual subtyping rules.
Ultimately, the operations you apply to Booleans are not the same as the ones you apply to Naturals and Integers, so, from the perspective of coherence, you should really consider them to be related by subtyping.