relative clauses with indefinite articles

In my view, the adjective clauses represent restrictive (essential) elements in your examples. As such, they SHOULDN’T be set off by any commas.

If all you want to say is, "They own a small shop" or "They're looking for an employee" and the info about what they sell or the duty of the employee is not important or secondary, why then even have it there and set off by the commas?

They own a small shop which sells a variety of products. defining
They own a small shop, which sells a variety of products. no comma allowed becase the relative clause modifies something still indefinite to the listener.

They're looking for an employee who will manage the accounts. defining
They're looking for an employee, who will will manage the accounts. -- no comma allowed by the same token

Without the comma, the relative clause adds information relevant to the specific kind of shop or employee that the speaker is talking about.
With the comma, the relative clause just adds parenthetical information.

I see them with the following meanings (in the same order as you gave them):

The kind of shop they own is one which sells a variety of products.
They own a small shop.  It so happens that the shop sells a variety of products.

They're looking for a certain kind of employee -- one who will (be able to) manage the accounts.
They're looking for an employee.  Once they find this employee, they will assign him the task of managing the accounts.  (It's stretching it, but this employee could even be someone they know -- someone who already is an employee, but who is temporarily somewhere else in the building.)

That said, the usual meaning in both cases is the one without the comma.  The presence of the comma makes us think hard about what the sentence could mean. 

CJ