First we can point that in French with capital letters, the accent is not compulsory, therefore École = Ecole; the word would still pronounce the same.

I don’t think there is a real strict agreement for acronyms (or initialisms) and you are free to use them as you wish but for moderation the general rules are:

• we always use capital letters
• we never retain the accents

Any large instance/company will follow as much as possible these rules.

For the pronunciation it is the same, there isn’t a real strict agreement but we pronounce the letters as they are written. the motivation is that acronyms are not meant to be used for representing each word but to give a shorter name to a fixed redundant set of words.

therefore ENS (for École Normale Supérieure), will pronounce as /ə/ (the French letter “e”)

This said if you pronounce /e/ or even write ÉNS it is not incorrect, but those who already use the acronym for a long time may feel uncomfortable. Also those attached to rules may bring the ones I described above.

Accents on capital letters must be written, they have a full orthographic status so writing Ecole, albeit frequent, is a mistake. See Accentuation des majuscules — Accents on upper-case letters

However, the rule is relaxed with most acronyms (or more precisely initialisms¹) with which accents are often traditionally omitted like with ENS and HEC.

See also: http://www.hec.ca/qualitecomm/chroniques/franstan/sigleaccentues.html

If the accent is not there, the pronunciation normally follows the rule so these initialisms are pronounced as “euh enn ess” /ə.ɛn.ɛs/ or “hache euh cé” /aʃ.ə.se/.

There are nevertheless some people that write the accent “ÉNS” and more rarely “HÉC” and thus pronounce “é enn ess” /e.ɛn.ɛs/ and “hache é cé” /aʃ.e.se/.

That said, ENS is often “pronounced” Ulm or Normale Sup’…

^{1 Thanks @laure for bringing that word to our knowledge}