Why are small cap and old style numerals not used in technical writing?
The answer lies in a combination of technology and efficiency. In the old days when all was typeset "by hand" and not electronically, switching between Roman numerals and old style ones was not difficult. When electronic publishing became available, typography as a whole was ruined because everyone thought they now could make professional looking typography on their own personal computer and laserwriter. For a long time the digital typefaces did not include old style numbers because the character sets were too small to include those (E.g. PostScript Type 1) but now with the unicode standard, much more is included in a single type face. Thus, for a long time one had to switch from one type face to another to include these effects. In LaTeX, this was a little easier as you point out than in, say, Word.

The use of old style numerals was thus partly lost through the "digital revolution" but I also think it was lost because they simply went out of fashion. As with everything else typography and ideas within typography changes over time. I am not sure that the loss is entirely due to the introduction of digital tools but this introduction was a sort of final "stab in the back" from which it is hard to recover. In fact we are still seeing the effects of the PC in many publications since everyone is now the typographer without knowing much about the trade.

So to cap off, in the scientific publishing world, where speed is a key ingredient, attention to these details have simply not been considered as worth the time. One therefore must look at publications with more aesthetic goals to find fine typography.