Especially since Heart's Eggs are (at least according to the wiki) something only possessed by children, and since those are where Charas come from... well, the whole system doesn't work if kids can't have Personas, which means they need to have Shadows.
All children have a Heart's Egg in Shugo Chara, though saying only children can have them isn't precisely 100% true.
When Suu fixed Nikaidou's Hearts' Egg, she told him that he could still meet his Chara again in the future, even with him being a grown man. And then at the end of the manga, both the Tadase from the future and Dia mentioned that Hearts' Eggs don't completely, permanently disappear. Kiseki apparently still exists for the adult Tadase in some form according to him and Dia tells Amu that Hearts' Eggs can be "born again, many, many times" even when they seem to be gone, which mirrors what Suu told Nikaidou.
So all children possess them and apparently usually "fade" when children grow up, but can reappear anytime if someone triggers the right conditions. Though, the only person we've actually seen do that on-screen is Amu herself at the end of the series, bringing back Ran, Miki and Su by diving into the Road of Stars (or when Suu fixed Nikaidou's egg, but that only lasted very temporarily).
How exactly that maps in this crossover quest is a good question.
We have a number of hints to how it works:
- The Chara System is artificial in this quest. The QM indicates Tsukasa, Tadase's father and Aruto were involved in its creation. It's been indicated the system was set up to deal with Overgrowth, the main symptom of which is psionic powers. The first exhibitor of such was Ikuto Tsukiyomi.
- Overgrowth does not stop you having a Persona. We know this, because Scavengers are apparently Persona-using Psionics given they require Persona Suppressants.
- Hotsuin knew what Shadows are, but didn't know anything about Charas. That strongly indicates Hearts' Eggs are not precisely the same thing as Shadows (otherwise he would know about Charas).
- Saaya having her Heart's Egg messed around with by Nikaidou and Lulu resulted in her being unable to birth a Chara.
- Amu's Charas double as her Personas.
So we know psionics can be either Persona-users or Chara-users, but what we don't have clear confirmation on is whether a Chara-user can also be a Persona-user, or whether the two are mutually exclusive.
If they are mutually exclusive, it is possible that Hearts' Eggs are just transmogrified Shadows and Charas are just butchered/mutated Personas. But if they are not mutually exclusive - if someone can have both a Persona and a Chara at a same time - that indicates a Heart's Egg has a greater degree of separation from a person's Shadow Self than that.
Meaning someone might not need to have a Shadow, in order to have a Heart's Egg.
EDIT: I guess what the question can really be boiled down to, ultimately, is:
"Exactly how artificial are Hearts' Eggs in this quest?"
ADDED TO AVOID TRIPLE-POSTING:
In all fairness, that's happened several times in her unwritten backstory. As you can see by this point, it isn't normally fatal.
Even if your mind isn't fully integrated, it still isn't likely to harm other parts of itself. Not that schizophrenia is all that great either, but for kids her age it's almost standard.
"Mhm." Ami's eyes were drooping. "He was really nice. He liked my rabbit."
'Rabbit?' Apparently there were things going on with Ami in her sleep. Her stuffed toy—Amu glanced down to check—was a seal.
....Wait.
Shit.
How many times has Ami already absorbed Shadows while Dreamwalking?
Was one of them Rei?