” Now, when we have a store that has some treif keilim we are mechuyav to assume that all the keilim are treif because they may have been washed together?”
If they were washes together with hot water, you have a problem.
“Same idea for cholov yisrael. Is there a source for the idea that we need to suspect that someone switched it?”
Someone in this very thread testified that exactly happened in a store she frequented.