"the application" ?
uninstalling h-e-n hostmode GUI for sure shall not cause any problems with boot.
h-e-n however rdepends on a feature that's provided e.g by kernel-power, which means you need to install kernel-power to be able to install h-e-n.
*)
Kernel-power is a linux kernel and uninstalling it obviously will leave your system in a broken state. Please refer to kernel-power howto, readme, FAQ, threads in this forum, etc. Basically "uninstalling" kernel-pwer means you are going to install the stock kernel. Never UNINSTALL a kernel!

This isn't related to h-e-n though


*) [edit] Depending on method to install hostmode GUI, this installation of kernel-power may happen automatically, and I heard a few minutes ago that fapman might also do a BAD thing and try to uninstall the kernel automatically on uninstalling hostmode GUI.
My take on this is: I introduced kernel hostmode API version, so GUI can check at runtime if the kernel has h-e-n patches or not. So I think the already implemented check for this version in hostmode GUI is sufficient and we should NOT rdepend on kernel-feature-hostmode. This would result in users getting a notifier "no compatible kernel found. Please install kernel-power!" (OWTTE) when starting h-e-n hostmode GUI.

Mohammad kinda disagrees on that, and has concerns about users getting even more confused if kernel-power doesn't get auto-installed on installing GUI.
So maybe it's up to you, users of h-e-n, to state clearly what you prefer.

/j