There's no reason to assume they weren't. If Freeza can clearly deduce what percentage he's using at any time, he'd definitely be able to note if battle damage limited his power or stamina. As for Goku, he'd been described as nearly out of Ki by the time he launched the Genki-Dama, so a 50x boost wasn't going to change anything if he was so fatigued.
The obvious answer is the meta one of plot convenience to drag the fight on, and a major reason why I prefer the Saiyan Arc's finale where we could easily see the damage chipping away at each character's stamina. If trying to find an in-universe explanation as to their power and stamina being just fine, it could be assumed the S-Cells' stimulation upon first activating Super Saiyan offers some level of a rejuvination affect. As for Freeza, I guess you could assume the damage from the Genki-Dama was just superficial.