Here, using “en” adds an emphasis on what you’re saying. And when you’re putting an emphasis on how long people take, you’re generally upset. But it doesn’t always express frustration.

It’s not just using “en“, it’s using both the pronoun and the nominal group. Here “en” acts as the pronoun, but it can be something else. I think it’s better to add a comma.

Tu en as mis, du temps ! = “tu as mis du temps” + “tu en as mis”

In the same way, you can say:

Tu aimes ça, manger, hein ? = “Tu aimes manger” + “tu aimes ça”

I’d translate this sentence as : “You really like eating, don’t you ?”(In the tone of a rhetorical question).

I would say that the language is a lot more familiar in the first sentence compared to the second one. I think the addition of “en” when you already have “du temps” makes the first sentence very familiar. If my primary school kids used the first sentence, I would correct them to remove “en” as unnecessary.

I disagree with @Teleporting Goat about the comma. That doesn’t work for me at all (being a native French speaker).

For the prepositions to use, I think both could work even in the second sentence, with a preference for “à”.