What benefits does it have to cover missing the shields?
The point with the stealth cruiser is to basicly use well timed stealth activation as a shield.
Being is stealth almost guarantees that any shot fired at you will miss. Of course, no enemy will fire at you when you're already in stealth. (In fact, their weapons won't even charge during this time.)
The trick is to activate you stealth after they have already fired, but before the shots hit you. This can be easier if you pause the game after you hear the shots, so you know wether you want to attempt to stealth, or just risk taking these paticular shots and save the stealth for later.
Alternatively, use the stealth early to make sure you have your weapons charged first, so that you also shoot first. Then just disable their weapons. But you need to sure you can disable all of them. (Or only leave them something useless, like ion weapons.)
Of course, this alone will not be enough to keep you alive later in the game. You'll most likely need to buy at least some shileds sooner or later.
Overall, the stealth cruiser is a rather high risk ship. Played well and with a bit of luck, you can down most early opponents without taking a single hit. But once you start taking hits, you usualy take a lot of them.
Stealth is better than shields. In the early game, enemies don't have that many weapons and (even in late game) don't coordinate them. The idea with stealth is that for some time it is near inconceivable that an enemy gets a shot in, and you try to make that period right after they shoot. Stealth gives near immunity to missiles and bombs. In that way, stealth is better than shields, which can be defeated with missiles, bombs or overwhelming fire (think burst laser 3, flak 2, etc.). It is actually a safe ship early on as you can take down the enemy's weapons system in the "first strike".
Anyway, even if I'm wrong in the first paragraph, the stealth cruiser (layout A) has a good arsenal, as the twin laser and mini beam can take down most enemies up to sector 5, and even using the twin laser alone, you can take down many early enemies.