why are capacitors often not labeled using engineering notation ? (1-999)
It is a matter of history, sadly. Capacitors where built well before the International System of measurement (SI) was established and some prefixes weren't used so much (e.g. nano).

For example, usually capacitors only used microfarad (sometimes written as \$MFD\$) and picofarad as units, this latter often written as micromicrofarad (\$\mu\mu F\$). Therefore \$10nF\$ could only be written as either \$10,000 pF\$ or \$0.01 \mu F\$.

Combine this with the need to encode other information on the smaller packages of the time (e.g. tolerance), and you end up with a metric ton of different encoding schemes, some more obscure than others.

Since old habits are hard to die, even in modern industry, the markings on the caps follow, in some way, the old tradition, where nanofarads "didn't exist".