1. Spelling conventions are different. It's almost certainly not the case that the pronunciation has changed since then, as evidence suggests that /si/ has been [ɕi] since Old Japanese in the 700s (and also suggests that /se/ was once [ɕe], meaning that the overall direction might well be from [ɕ] to [s] rather than the other way around). Some romanisation systems (such as Hepburn) prefer to represent as accurate a pronunciation as can be conveyed in letters (hence ‹shi›); other systems prefer either internal regularity or 1:1 phoneme-to-letter correspondences (giving ‹si› to be consistent with ‹sa› etc). These days the most common system for names is some variant of Hepburn; this was not always the case in the past (which is likely why your mathematician's name isn't in proper Hepburn).
2. As for the accent, my (admittedly non-native) gut instinct suggests [jòɕídá] or [jòɕídà] and [kóòsàkù]. Others can correct me.