I decided to re-install and try another run, this time without SCS. After installing BG2, I checked NearInfinity to see the state of Irenicus' dungeon. Wouldn't you know it, Malaaq was already there in the vanilla dungeon without any mods applied. However, when I took a test character through the library, he did NOT appear. 

Can't be as bad as the bug I found last year - where Torgal's bodyguards wouldn't die. I abandoned that playthrough shortly after. At least that bug got fixed.

I always install "Pause all dialogues". Anyway I've long since left the dungeon and am currently building up enough levels and equipment to take on Firkraag.

Yeah, I don't mind so much the extra equipment. I can use them, sell them, or ignore them. Malaaq, however, initiates dialogue the instant he sees me. Since I'm still in combat in the library when that happens, it's damned distracting. Plus the djinn appearing outside the Plane of Air offends my sense of orderliness. As far as I can tell, the script that summons Malaaq when you click on his flask should still work so maybe I'll just delete him from the dungeon the next time I do a Trilogy playthrough.

According to Malaaq's DLG, he's supposed to hand over whatever he's carrying. The only thing he's carrying is the Sword of Chaos (no Varscona), which he gave me. The cambion (IDEMON01.CRE or IDEMON02.CRE) was also wielding the Sword of Chaos, which he duly dropped when I killed him.

I also checked the relevant ARE files. AR0602 (Irenicus' Dungeon level 1) has Malaaq hanging out just outside the library, exactly where I found him. Nothing happened when I clicked on Malaaq's flask, but that may be because I had already complete his quest by the time I entered the Plane of Air.

Apologies for taking so long to get back to this. I'm playing in standard single player mode.

I ran the change-log tracker suggested for both the cambion and Malaaq and got back these results:

The readme of arestoratonp was probably the one place I didn't think of checking. Not that it gives any indication that it tinkers with either Malaaq or the cambion. I'll also note that it says that Malaaq was supposed to hand me an additional weapon, which I recall ever getting. (Maybe that's where I got the other Varsonca?)

Running classic BGT (not EE), I've finally transitioned to BG2. I was quite surprised when I stumbled on Malaaq the djinn just outside the library, rather than in his flask in the Plane of Air. His dialogue was otherwise unchanged and he gave me the Sword of Chaos after I retrieved the flask for him. However, the cambion also dropped a Sword of Chaos, so now I'm running around with two Swords of Chaos. I've also somehow acquired two Longswords +2 Varscona.

Some of the mods I'm running:

bg2fixpack

bgt

bgttweaks

cdtweaks

stratagems

ub

atweaks

turambar_fixes_tweaks

d0tweak

I've run this set of mods before without ever encountering this problem. Full weidu.log attached.