I have large colonies of RCS in both of my tanks, one with a male betta, one with a sorority. I have only occasionally lost a shrimp. Just have plenty of cover (particularly java moss, or other plants that grow densely like lacefern and elodea). In a sparsely planted tank, sure, shrimp aren't a great idea with a betta, but it is perfectly doable. Don't be put off by it. :)
And I agree, those black spot aren't something to worry about.