How exactly did all those powerup cans (which, in-universe, are being made by Hoodlums) get into places like Knaarens' caves or the top of the tower of Leptys?
The Former: Some Hoodlums tried to invade the Caverns, But the Kanaaren got to them. The Latter: The Hoodlums invaded the Tower of Leptys, so they left some lying around.
Why do Hoodlums NEVER actually use these powerup cans if they are making them and even hold them from time to time?
Maybe they do, and it just has different effects than Rayman or use them differently. We do see enemies that would fit the power up description. For example, the big, bulky enemies with the armour could be Red, The flying enemies could be Yellow, ect.
The power-up Cans and cages in the Knaaren Caverns would suggest Hoodlums were indeed inside the caverns, yet there is not a single hoodlum in said caverns. Considering how hostile the Knaaren are, especially towards folk not their own, that would mean all the Hoodlums may have been killed by the Knaaren.
For that matter, if the Tower of Leptys is Knaaren territory, where the hell are they? Considering Reflux stole the sceptre for his own gain and teamed up with Andre, wouldn't that mean Reflux committed a mass genocide of them, his own species, simply out of petty spite? Damn.