Actually, when it is decided to wrap this series up, a proper relationship between them will be part of the outcome. But, until that time, shyness and deference will keep them from expressing their reciprocal love.
In the context of this particular story. ‘M’ can reasonably be read as standing for “masochist”; but the Japanese tend use ‘M’ both for masochist and for submissive, and (correspondingly) ‘S’ both for sadist and for dominant.