First, in many cases, creature's are under control of the builder. A monster with +5 con and another monster with +2 con and a +3 save proficiency are identical -- the +2 con one can just have more HP.
Second, for attack stats, increasing your attack stat gives you higher accuracy. While granting save proficiency doesn't. A monster that misses all of the time is boring; so deciding between +5 strength and +2 strength +3 proficiency, going with +5 strength works.
Save proficiencies (and skills) makes the stat block very slightly more complex. You get more bang for the complexity buck if you drop it all things being equal; especially with low modifiers. A +2 bonus has less information:math than a +6 bonus does, so adding save proficiencies (or skill proficiency) has better bang:buck at higher CRs.
...
There may be deeper reasons. For example, lagging of save proficiencies from CR 1-8 would result in spellcasters gaining in power-per-action. If then save proficiencies became more common from CR 9-30, this happens around the same time that spellcasters start getting their level 5+ spells (which are a phase change in what they can do).
Meanwhile weapon based PCs "whiteroom" scaling is different, with a power bump at 5, and a flattening off at level 10+. With spellcasters running into DC walls at the same time that weapon users power curve flattens out, it could produce balance.
But I haven't done any math to prove that, nor evidence that even if it did happen it was intentional.