She puts alot of stock on those clones. Of course, she has a real good reason for it.
so they can talk...each one is essentially Samus with her full array of powers and Varia suit...and on top of that they can clone themselves into an army in a matter of hours. Man, this is just ten flavors of "not good" isn't it?
Samus isn't COMPLETELY without weapons; She still has her emergency pistol. Of course, that's even worse than the power beam even when it's fully charged, so yeah, she's screwed. They seriously need to get off planet for a while to re-arm. Either that, or find a Chozo statue that has a spare Power Suit, a battle robot body that Duo's AI could occupy, and something for Chrono to draw his magic from. As for how they get to it past the bad guys, that's what the Space Pirates that Marle and Lucca now control are for. They could use them as Red Shirts!
evil wwill win!!!!