Thank you for posting scans of the cards! Team Aqua's Secret Base and Team Aqua's Muk each at [C] to that Retreat Cost of each Pokemon in play, except for Team Aqua Pokemon. The effects do stack with each other. In addition, if you had multiple Team Aqua's Muk in play, they would also stack. So, if you had two Team Aqua's Muk and Team Aqua's Secret Base in play, each non-Aqua Pokemon in play would require three extra Energy to retreat.
An exception to this was if a Pokemon had an effect on it that caused it to have no Retreat Cost, such as if it had a Float Stone attached. Setting a Retreat Cost to zero is not the same as adding or subtracting to it. If an effect states that a Pokemon "has no Retreat Cost," then it would not be affected by Team Aqua's Secret Base or Team Aqua's Muk.