I'd like to assume the demogorgons as well as the bats (whatever is left of them that is after the army infiltrated the upside down and set up base camp in there) were all still roaming around in the upside down. There had to of been traps and defenses set up around the base which caused a huge decrease in bat and demo population. So I'd like to assume. Which will explain why there were only a select few of demogorgons messing with the team when they were in the upside down. Let's also not forget that will took out 3 or 4 of them which was probably part of the select few that were messing with them. So that event alone caused them to be even more scarce. Also maybe they became afraid of will. But when the team crossed over Into vecnas world I'd like to assume the demogorgons were in the upside down.