If Mordekaiser, Dominating is moving to attack a battlefield that my Akali, Silent is located at, can Mordekaiser choose Akali, Silent with his ability?

Yes — Mordekaiser, Dominating can kill Akali, Silent with his attack trigger.

Akali's protection only applies while she isn't in combat. When Mordekaiser moves in and combat opens, Attacker/Defender designations are assigned (Rule 466.2.c.3) before attack triggers are put on the Chain (466.2.d, Rule 383.4.e.2) — so by the time you finalize Mordekaiser's trigger, Akali holds the Defender designation and is a legal choice (same logic as FAQ #12619). You do need to actually discard 1 to kill her, since the trigger is optional.

One contrast worth remembering: if Mordekaiser instead gets played (e.g., Ambushed in) rather than attacking, his "when you play me" trigger finalizes before any combat exists, so Akali would be untargetable at that moment.