In what follows, let $R$ denote the real line object of Smooth Infinitesimal Analysis (SIA).
You can of course define the function $f : R\setminus \{0\} \rightarrow R$. The domain of this function is $R\setminus \{0\}$, i.e. $\{ x \in R \:|\: x \neq 0 \}$.
The function $y \mapsto \frac{1}{y}$ is defined on the object $R \setminus \{0\}$ by the standard axioms characterizing $R$ in SIA. Similarly, you have functions $y \mapsto \sin(y)$ and $(x,y) \mapsto x\cdot y$ defined on all of $R$, so the composition $y \mapsto \sin(y) \cdot \frac{1}{y}$ defines a function of signature $R \setminus \{0\} \rightarrow R$ as expected.
The fact that you cannot write $R$ as $R \setminus \{0\} \cup \{0\}$, while true, is not a particularly relevant consideration here.
2.
No, if $\mathbb{R}$ denotes the set of (Dedekind or Cauchy) reals, you cannot prove that $\mathbb{R}$ coincides with $\mathbb{R}\setminus \{0\} \cup \{0\}$ in any intuitionistic or constructive set theory.
3.
You can define the function $g$ by cases as you do above. The domain of the function $g$ defined this way will be $R\setminus \{0\} \cup \{0\}$, however. What does this mean? It means you can apply $g$ to:
- any $x \in R \setminus \{0\}$, i.e. any $x\in R$ for which $x \neq 0$ holds; and
- any $x \in \{0\}$, i.e. any $x \in R$ for which $x = 0$ holds (we have a unique such $x$).
However, you cannot apply $g$ to an $x$ for which you cannot establish either of the above. In particular, you cannot write $g(\varepsilon)$ for some nilsquare infinitesimal $\varepsilon^2 = 0$, unless you also know that $\varepsilon = 0$ holds.
4,5,6.
Normally, when we work in smooth infinitesimal analysis, we assume that we have access to all smooth functions on $\mathbb{R}$ as functions $f: R \rightarrow R$: this amounts to saying that $R$ constitutes a smooth algebra. You don't ever have to worry about whether some smooth function is definable in SIA: the answer is always yes, pretty much by definition, and these smooth functions work on infinitesimals exactly the way that the respective Maclaurin series suggest.
Of course, if you want to use Smooth Infinitesimal Analysis as a sort of pure axiomatic "foundation" for calculus, this approach does not work: figuring out which functions are the smooth ones is part of the work that a foundation should let us do. But even if you use SIA this way, you still have the integration axioms and the implicit function theorem, which allows constructing many of the familiar smooth functions one would want on $R$.
The question of limits is similarly complicated. Different methods apply depending on what your goal is, and some approaches involve working with models of Smooth Infinitesimal Analysis containing both nilpotent infinitesimals and invertible infinitesimals. And since most users of SDG don't often need limits for any purpose, it's also necessarily a niche topic. While it might work as a separate question, I suggest coming back to it after working through one or more textbooks on Smooth Infinitesimal Analysis or Synthetic Differential Geometry. This would preferably include Moerdijk-Reyes, but fully understanding how Bell does things (without limits) would also provide good context.