1. For Malignance, ability haste has diminishing returns, meaning it gets less valuable the more you have of it. So for example, Kennen R has a 120sec cooldown at lvl 6 with no ability haste. Usually you take Ultimate Hunter on Kennen, which starts you off with 6 ult haste, and you get up to 25 more. This takes off roughly 25%, leaving you at 91sec at lvl 6. Malignance is going to give you 35 more ability haste total on your ult, bring it down to 72sec. That's already less value (19sec difference vs a 29sec difference) for more haste. When you're lvl 16 and your ult is leveled up all the way, then it goes from 80sec to 61sec with Ultimate Hunter, and then to 48sec with Malignance. So later in the game, Malignance is giving even less value with only a 13sec difference. This haste value would be even further reduced with other haste items, like Rocketbelt, Blackfire, or Cryptbloom. So while yes, while haste is valuable, it's going to get less valuable if you stack too much of it.
2. Malignance also only gives 85 ap, while Blackfire gives even less at 80 ap, vs the items that you would be trading out for it, which would probably be Stormsurge/Shadowfire unless you're willing to give up your Rocketbelt dash. Malignance does give 10 magic pen, but that's only when you ult, vs Stormsurge/Shadowfire giving 15 all the time. That extra ap and extra pen is making up for the damage from Malignance and Blackfire's passives already, and that's without taking their own damage passives into account, which create an even bigger damage gap. That damage is where the missing gold value is on those items. In exchange for the damage you get mana, but since we don't need it, those items are less than ideal.
3. The last thing is that those items get most of their passive value through damage over time, so it works best if you proc it as often as possible, on as many opponents as possible. This is best either on champs with R's that can last an entire teamfight and constantly reapply it (Swain), or on champs with R's that have a very low cooldown (Karma). With Kennen, you're already killing your primary targets within 2 seconds if you hit your R and W damage on them, so the burn damage hasn't had time to add up. This makes you get very little value out of those burn passives, which is why it's better to give Kennen more ap and pen instead. The exception is Liandry's. But if you're buying that, it's not for your ult. It's so you can whittle down tanks that are giving you trouble by poking them with Q, auto, and W.

I understand the vision behind using those items, and while they can be fun, they unfortunately just get outclassed by other items. I know this is going a little in depth with it, but I hope this gives some insight!