Recently there's been an increase in the number of convenience stories that sell medicine, but the number is still low.
There are more convenience stores selling medicine than before, but there still aren't all that many.
「not all that many」は「そんなに多くない」「それほど多くない」という意味です。
扱う=to sell, to deal in
例文1はちょっとニュースっぽい言い方です。「there's been an increase in」や「the number is still low」はニュースで使いそうな表現ですので、例文2はもっと会話的な言い方です。