It means "Was there (any) coffee?", inquiring about the presence of coffee, not whether something is coffee.
"Er det kaffe" is preferable, especially if you've just had a taste, but in cases where you've finished drinking something and then ask, "Var det kaffe?" would work.
Why is there an es? I don't find one here: http://www.verbix.com/webverbix/go.php?T1=finne&Submit=Go&D1=25&H1=125
What is this verb's Infinitive, å finne?