In the following I assume that some basic mathematical requirements are fulfilled, like continuous and differentiable observables.
When you try to embed a system, you use $m$ observables $x_1, …, x_m$ trying to represent the dynamical state of the system. $m$ is called embedding dimension and if it is sufficiently high (and you have used appropriate observables), your representation fully captures the system’s state (e.g., exactly knowing $x(t)$ suffices to predict $x(τ)$ for any $τ>t$) in a continuous manner (e.g., $x(τ)$ can be continously mapped to $x(t)$). In this case, the representation is an embedding. E.g., the right part of this figure is an embedding of a sine wave using position and velocity as observables, and this figure is an embedding of a Lorenz system with $m=3$. Takens, Cao, Liebert and Kennel and others now tried to answer the question of what are appropriate observables and what is a sufficiently high $m$ for a system of which you only have a time series.
The strong Whitney embedding theorem (applied to this problem) basically says that if your system’s dynamics is governed by $d$ differential equations, there exists an embedding with $m=2d$. This is not very helpful, since we neither know $d$ nor how to embed, i.e., which observables to use. The weak Whitney embedding theorem states, that almost every representation with $m≥2d+1$ is an embedding. This is better, but you still need $m$ independent observables ($m$ dependent observables are one of the reasons why it is only “almost all”). Takens now found, that representing the phase space using only one observable at $m$ different times is almost always an embedding if $m≥2d+1$. And this finally is helpful, apart from the fact that we do not know $d$. Also representations with $m<2d$ may be an embedding, e.g., you need $d=2$ to generate a time series $\sin(t) + \sin(αt)$ with $α∈ℝ\backslashℚ$ and the corresponding phase space (a torus) can be embedded with $m=3$.
So there exists a smallest dimension for which there is an embedding and this optimal embedding dimension is $2d+1$ or smaller. We now want to use an embedding that is equal or not much larger than this optimal embedding dimension, since an overly high embedding dimension makes analysis more difficult. We would not need to perform time-series analysis, if we already knew the system sufficiently well to tell its optimal embedding dimension, so we can only estimate it with several techniques that you already named, which all have their advantages and disadvantages. So there cannot be a definite answer to questions 1 and 4.
As for question 2, there are several fractal dimensions that may be used to characterise systems, e.g., the Hausdorff dimension, the box-counting dimension or the correlation dimension. Their values are $d$ (and thus integer) for linear systems, non-integer for most non-linear systems and infinity (or not properly defined) for stochastic systems. Also their values are usually close to each other for one system. The corresponding concepts are so entirely different from the embedding dimension that it’s hard to name differences. At least for the pendulum, it is easy to see, that $d=1$ and $m=2$ is the optimal embedding dimension.
Question 3: For every aspect of your dynamics, there is a filter that may destroy the corresponding information in a time series. E.g., a low-pass filter may destroy the effects high-frequency dynamical noise the same way as it destroys high-frequency observational noise, and thus make a stochastic (i.e., infinite-dimensional) system look finite-dimensional. So, the best you can do is select an appropriate filter that should not destroy anything and argue that it does. Even then, you cannot distinguish between high finite dimensionality and infinite dimensionality. So only, if you find low finite dimensionality, you can make such a statement. There are several characteristics that may be useful and all should be compared to the respective results for appropriate time-series surrogates and should not depend on $m$. Anyway, if you do not want to calculate the dimension, but only show that it is finite, it suffices to show that the system is not stochastic (what I said about filters and surrogates, still applies).