Is it OK to use 只 (only) when it already uses 只 as a measure word?
"只有20-30万只蜜蜂" is a valid sentence in simplified Chinese. You just have to read the two 只 differently, because they have different meanings.


The first "只" in the sentence means "only" in both simplified and traditional Chinese and it is read as /zhi3/.  (It can also be written as "祇" in traditional Chinese) 
The second "只" in the sentence, is the simplified version of 隻 (classifier for certain animals) and it is read as /zhi1/


The sentence "只有20-30万只蜜蜂" is actually "祇有20-30萬隻蜜蜂" in traditional Chinese characters.