1. Will carbon content of the column material influences the retention time of the molecule, if so how?
If two columns have the same specific surface and porosity, and if reversed-phase is the dominant retention mechanism, then retention time will be longer on the column with the higher carbon loading. Note that the first condition is rarely met, and so carbon load, by itself, provides little useful information.
2. What is the role of SDS as ion-pairing reagent in improving the retention of highly ionized molecules (mobile phase also contains pH 3.5 buffer, TBA+ and acetonitrile)?
The use of both anionic (SDS) and cationic (TBA) ion-pair reagents simultaneously is unusual. The effect on retention in such a system can be anything, depending on the charge and pKa of the analyte.
3
. Amoung the amide C16 column and RP C18, which is preferred for a highly ionized molecule?
That depends on the pH, the pKa of the ionized molecule, on what you are trying to separate it from, and on whether or not you use ion-pair reagents.
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