Is there a way to get more money in the game?
By picking Joy + Phil + Snow and get the Gold Digger bonus 3 times.
Seriously, killing all the enemies does help, but if you want to complete the game without ever dying, you might have to "buy smart", ie choose what to buy.
Also, how come the items can only be bought a number of limited times only?
For the strategic aspect.
It's also more realistic.

I noticed that I can’t buy a lot of restoring items and I have been using them. So now, I might reload from the beginning to make sure I get enough for the later part of the game.
Or you can finish the game without aiming at everything being perfect?
Also, does the mode you pick determine whether you get a good ending or is it just for bonus characters only?
Yes, the mode has an influence on the ending picture. It also determines, indeed, which bonus character you may get.