This will sound more than a bit odd, but I think a great deal of the story's Holocaust references are part of a broader satire of anti-feminist discourse, framing abortion in terms of genocide -- perhaps riffing on the then-popular smear "feminazi". Four points:

1. On page 6140, Spades Slick (abbreviated SS) commands all of the Felt to get in the oven. A few readers observed that this page was published on that year's Yom HaShoah (Holocaust Remembrance Day) and wondered whether this was a reference to gas chambers or crematoriums -- like a fucked up version of the story's Christmas-time alchemy binges or New Year ball-drops (Jade and Jane's towers).

2. Assuming the above isn't a one-off joke, it becomes interesting that the Sea Hitler who exterminated most the human race is also known as Betty Crocker, a purveyor of baked goods. Meenah actually makes a point of framing baking as murder on 4755 before she tries to kill Roxy: "ever do any baking nerd // ... // then you know -EXACTLY what you do with somefin thats done // you stick a fork in it" This anecdote colors the term "grubloaf" -- Alternia culls its infants on a scale that allows them to become mass commodities like Nepeta's paints, and the invocation of baking connects their deaths to other discourses on ovens vis-a-vis genocide.

3. GAMEBRO magazine is a farcical example of hypermasculine attitudes in gaming circles, but its title is also riff on the respectable periodical PLAYBOY -- GAMEBRO's glib dismissal of girly shit therefore hints at some form of engagement with feminist critique of porn as a bastion of misogyny. This makes it less surprising that when we meet the character Bro, he seems to chiefly occupy himself with producing pornography (that it's GAY pornography complicates things but the story's engagement with homophobia is a separate discussion). The point being, we should understand that Alternia's GAMEGRUB is likewise an implicit porn magazine -- one that deals in images of dead babies. It flips the feminist critique of porn and makes the pejorative proposition that in Sea Hitler's world, abortion is the new sexual fixation.

4. Wrt to Vriska saying "88" on 5396, I think it matters that the "bait" in question is, in her own words, "dead children". The big bad has 88 for eyes whenever the black billiard balls settle, giving him a loose link to the Nazi discourse. He comes from a species of skeletons which in combination with the name "cherub" suggests dead infants with angel wings -- which we now might associate with Caliborn's (abandoned) title "Eternity's Shylock" or his reference to the Merchant of Venice via the "pound of smut" line, given the invective-based association of the Holocaust (and therefore other invocations of antisemitism) with abortion. And the name "Lord English" has synonyms in the form of variations on "large utterance" -- "Imperial Drone" (which collects the "genetic material" ie blood of children) and "Vast Glub" (which causes mass killings) are major ones, but in the context of anti-feminist discourse, I would be remiss not to include "Huge Bitch". That the Bitch's 88 would be dead children seems consistent with the joke at the core of GAMEGRUB magazine.

...is my current sense of things. Not sure if this really puts anybody's concerns to rest (or if any of you will find this persuasive), but personally I find Homestuck's absurdly abstract parodies of reactionary discourse to be fascinating.