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During method selection our chromatographists have options like NH4, TFA, Formic Acid. What's the point of choosing only between acid? Why not use the strongest that guarantees ionization? The sample contains small organic molecules.
And if the analyte is an acid, don't we want to have a base as a modifier? Otherwise how can we ionize it using ESI?
Stanislav, that is a Nobel Prize winning question. In short, nobody knows nitty-gritty details of how the electrospray ionization imparts a charge to the analyte. When Fenn (reinvented) the electrospray phenomenon and used for ionizing large biomolecules he was shocked and gave an analogy that it is like making the elephants fly. He got a Nobel Prize as well and a lot of patent issues in the university. There are three electrospray ionization models, you can read on Wikipedia, https://en.wikipedia.org/wiki/Electrospray_ionization#Ionization_mechanism
The key point in electrospray is that you need an electrolyte (forget about acids or bases). All you need is a conducting liquid between the electrode to generate the electrospray. In that process, the ion is created. There are studies, I am sure, on the effect of pH on the efficiency of ionization. I can tell what to avoid in electrospray: TFA (because it forms ion pairs), hexanes, all other pure non-conducting organic solvents. So you you can get the point that ionization in the solution has little to do with ionization in the electrospray.
Now coming to your chromatography part, which is purely empirical. The reason for avoiding bases in mobile phases is that it they will eat (=dissolve) the silica columns. Silica is not pH stable above 8. Silica based HPLC columns can tolerate low pH like 2.5, and below that the bonded starts to peel off, e.g. if you use a C-18 column and use pH 1, it will become a bare silica in a few days.
