For the IHÉS, I have heard both, and often seen it written IHES, since getting the accented capitals is tricky on many computers. But since according to the Académie, the capitals should always be accented (see Accentuation des majuscules) it may be considered wrong (or non-standard if you are descriptivist).

Anyway, the only thing you should worry about is mutual understanding. Depending on the context you may say Institut, or Institut des Hautes Études, which are not much more complicated to say than either IHES or IHÉS.