What does "find someone well" mean?

It means "I hope this email arrives at a time when you are well (healthy, happy, etc)"

In other words, "I hope you are doing well." It is not a question, it is just offering nice wishes.

kmote gives the correct sense of well as used in the expression, and John Lawler points out that nowadays it's highly formal (tending to pretentious).

However, this usage of find with object and secondary predication (the adjective well) is quite commonly used:

we ... found him well and in high spirits

I found him well and hearty

I had found him well and looking forward to release

they found him well and in good heart

they found him well and flourishing

I found him well and hard at work

I found him well and every thing all right

(Google search for "found him well"; all above in first 10 results in my search; slightly tidied)

Notice that well does not appear alone in these predicative structures: either it is coordinated, or 'him well' (the last example) is. It would not be wrong without coordination, but appears far less usual. That this is possibly to avoid confusion with the adverbial sense of well (which possible confusion prompted the original question) is evidenced by the fact that "found him unwell", "found him ill", and "found him in high spirits" and the like can and often do stand alone. However, "found him hearty" doesn't sound natural to me - but then hearty is archaic in all but a few usages. "Found him flourishing" also sounds unnatural. It seems idiosyncratic.