Maximal munch rule issue for lexers: is detection decidable?
To answer in the large, the fact that the syntax of programming languages is not context-free is not news (see e.g. Floyd, 1962).

To answer more precisely, in a context of scannerless parsing like yours, a way to implement maximal munch is to employ so-called follow restrictions (van den Brand et al., 2002) by forbidding some language to follow a given rule.  In your example, you could write a restriction X -/- a forbidding an $a$ after the token $X$.  Provided your forbidden languages are regular, these restrictions can be compiled back into the grammar (however in van den Brand et al.'s formalism, the forbidden language can be context-free and $X$ can be any nonterminal, and this clearly leads to an undecidable emptiness problem).

Another formalism for scannerless parsing is that of parsing expression grammars (Ford, 2004), which has a greedy, maximal-munch type semantics, and an undecidable emptiness problem.

Now, it doesn't look like your specific maximal munch semantics would allow you to reduce from these undecidable problems.  For a start, it seems to me that, rather than emptiness of the generated language, a tool should more broadly warn the user about any case where a token might "eat" a (non-empty) prefix of its follow language, i.e. whenever $(L_T\cdot\mathrm{Pref}_+(L_R))\cap L_T\neq\emptyset$, regardless of whether this prefix is mandatory of not.  This would capture your $aba^\ast b^\ast ab$ example if I understand correctly how you would tokenize it.

To conclude, here is an attempt to formalize your notion of maximal-munch-caused emptiness: let $\langle N,T,P,S\rangle$ be a context-free grammar with nonterminal alphabet $N$, terminal alphabet $T$, production set $P$ and axiom $S$.  Each terminal symbol $X\in T$ is associated with a regular language $L_X\subseteq\Sigma^\ast$ used for its tokenization.  For every occurrence of a terminal symbol $X$ in some production $A\to \alpha X\beta$ of your grammar where $\alpha,\beta$ are sequences of mixed terminals and nonterminals, construct the follow language $L_{\beta,A}$ of this particular occurrence (this is a context-free language) and consider the residual language of the token $L^{\text{max-munch}}_X=(L_X^{-1}\cdot L_X)\cap\Sigma^+$, which is a regular language of strings that will be "eaten up" by the maximal munch semantics.  In fact the language $L^{\text{max-munch}}_X$ is the language one would put in the follow restriction for $X$.  Then, if $$L_{\beta,A}\subseteq L^{\text{max-munch}}_X\cdot\Sigma^\ast\;,$$ or equivalently $L_{\beta,A}\cap (\Sigma^\ast\backslash(L^{\text{max-munch}}_X\cdot\Sigma^\ast))=\emptyset$, any string allowed to follow this occurrence of $X$ will be "eaten", and the language of the rule $A\to\alpha X\beta$ is empty.  Using the classical algorithm for emptiness checking with this extra twist for handling terminal symbols might solve your emptiness problem.