That's one thing that bothers me about the bombardment deck. I'm probably going to house-rule that after the set-up draws the deck gets reshuffled and again during the each order draw phase.
You can do that if you want a random result (in fact, if you really want a random result, you can use a combat result table instead and throw dice, or shuffle the deck between every draw).
The way it is with this deck however also balances things out a bit in the short run: Long-term distributions of results are exactly the same, but in the short term, if individual cards are always either better for the imperial or the traitor player (and not one aspect of a card is different from another, like eagle cards with high bombardment values and breach would be), this means that you can count on every "cluster" of 32 random results being fair for both sides.
So it retains the same random results overall, but reduces standard deviation and variance for both sides - essentially yielding both a bit less randomness and better predictability towards the end of a stack, and less runs of good random results only for one side.
In short, using cards instead of dice makes things more fair in the short (cluster of 32 random choices) term.
Edit: If on the other hand you shuffle the deck every so often between the times the deck runs out, you increase randomness a lot and also increase standard deviation and variance over and above if you'd use dice or shuffle between every draw. You'll make things a lot more wildly random and increase the odds of one side winning through lucky draws. If that's what you want, fine. If it isn't and you want to value skill over luck, shuffle only when the deck runs out.
2nd edit: This is assuming that indeed individual cards are either benefitting the imperial or the traitor player overall. If they're mixed, it's all out of the window. I haven't checked.