The HCS Navy's key role is intended to be the major way the HCS can fight back against a land invasion of Cloneworld if HCSAF facilties have been badly degraded by orbital bombardment. The focus of the navy is to maintain the ability to strike back against an invader and it is doing this by developing submarine launched cruise and ballistic missiles and airpower from it's carriers.
At the moment ships are hard to hit from orbit especially when mobile but it is feared that advances in technology could negate that. The HCS are thus working on "orbital stealth", measures to hide ships from detection by orbital based weapons. One way is to reduce the wake created by ships and a "top side cloaking field" which will use cloaking technology to hide signatures from prying eyes.
The HCSN hope to have these measures in place by the end of this decade.