Magic pen marks aren't very good because they wear off quickly. Btw, if you actually read my items comments, I recommend banshee's veil too if you are having trouble with ap characters.

I've been playing malphite since he was 300 speed, with the old form of brutal strikes, 12 second cooldown on shard, etc. What I've been noticing in games is that opponents building magic resist are really hard to kill with your abilities, but may be easy to kill with phys, manamune is just one of many items you can take to counter that and since you're mana at level 18 with a frozen heart and possibly a banshee's is so high, it has high damage.

Defensive marks are, in general, terrible. The bonuses they give are really not that noticeable, so you'd really be a lot better off getting magic penetration marks. You don't need Manamune either. Malphite gets off fine with Catalyst, which can be built into a Banshee's Veil later. Veil is a great item on Malphite, and I recommend it here.