Hello, Zizi, and welcome to the Grammar Exchange.
I agree with Ahmed_btm's answer: the singular verb is needed in each case. Grammatically, "combined with" does not function like "and." Of course, if you replaced "combined with" with "and," you would need plural verbs:
3. Effortless website navigation and shorter hold times empower your users and increase engagement across all your digital platforms.
As Ahmed pointed out, however, the combined with phrase modifies "website navigation," as can be seen by fronting the phrase "combined with shorter hold times." Here is another way to see how the two phrases interrelate:
4. When effortless website navigation is combined with shorter hold times, it empowers your users and increases engagement across all your digital platforms.