Abbreviations, initialisms, and other short-forms can be can confuse those without context. Be explicit to avoid such confusion:
Use the long-form once, followed by the abbreviation in parenthesis, then use the short-form.
Arrakis, also known as (AKA) Dune, …
…
Leto Atreides the Second, aka God-Emperor, …
Provide context around the short-form. E.g. a link, footnote, HTML abbr tag (a), etc.
Arrakis, AKA (a) Dune, is the desert world at the center of the Dune series by Frank Herbert.
Avoid the short-form. Instead, use the long-form exclusively.
Arrakis, also known as Dune, …
…
Leto Atreides the Second, also known as God-Emperor, …