Do reputable journals ever conduct peer review entirely by email?
I have interacted with several reputable math/TCS journals, both as author and as reviewer, entirely via email without the involvement of an online submission. I have even witnessed senior members of the community expressing the sentiment that they never agree to the semi-automated referee requests sent by online submission systems, but only to referee requests sent "by hand".

Summary: Yes, there exist reputable journals conducting peer review entirely by email.

Now whether or not a journal soliciting peer review without an online submission system is more likely to be disreputable than one that does, I do not know. I see no particular reason to assume either way.