When referring to a particular atom, both in text and when using a graphical representation, several conventions are being applied.
In the field of crystallography an arabic numeral either follows the element symbol without any space, e.g. $\mathrm{C}42$ for carbon atom number $42$ (usually assigned during solve/refine routine by SHELX), or is being placed in braces, e.g. $\mathrm{C}(42).$ Sometimes hydrogens attached to the same carbon atom inherit its number and receive an additional letter, e.g. $\mathrm{H42c}$ for the third hydrogen in $\mathrm{C42}$ methyl group.
In NMR spectroscopy an element is normally labeled with a script-sized symbol (arabic number or lowercase letter) in the bottom right corner, e.g. $\ce{H_3}$ or $\ce{H_c}.$ Mestrelab Mnova places numerical labels underneath the element symbol, e.g. $\underset{3}{\ce{H}}$, or directly in place of the element if the symbol for the latter is hidden (carbon, in most cases): ${\scriptsize 3}.$
These labeling schemes used in both instrumental methods (which I cherry-picked solely for the illustrative purposes) seem to work OK in a sense that they are compatible with expanded AZE-notation required to depict any element and its attributes, such as chemical symbol $\ce{El},$ mass number $A,$ atomic number $Z,$ oxidation number O.N., charge $q$ and number of atoms of given kind $x$:
$$\Large\ce{\overset{\text{O.N.}}{^{$A$}_{$Z$}El^{$q$}_x}}$$
and won't cause any confusion (except for $\ce{H_3},$ maybe). However, it would be nice to know whether there is a standardized way to attribute a label to an element that can be uniformly displayed and recognized (main text, titles, structures, illustrations etc.). Does such robust labeling scheme exist?
P.S. If you are a software developer and read this, also feel free to comment or add an answer as to which labeling scheme you've came up with for calling out a particular atom.