Taking a side trip here between Bilbao and San Sebastian was a wild goose chase for us. The drive through the hills and along the coast is pretty, but tiring. Lekeitio is hardly a charming fishing village, it's surrounded by high-rise apartment buildings. Unless you love being in the car, I think time would be better spent getting to your destination many hours earlier, less fatigued and spending time out of the car.
Last summer, we rented an Airbnb place in Lekeitio for 3 nights. I can see your point if Lekeitio is just a day visit, but for a few days, it was lovely. We were there in late June before all the tourists arrived, so the beach was nearly empty, but the weather was good. My son is a runner and he trained while there. It was a nice quiet place to run. There isn't a lot to do in Lekeitio, but at the beginning of a trip that included Bilbao, San Sebastian, and Barcelona it was a nice breather. I enjoyed the seafood in the restaurants along the port. My husband got some great photographs of the village. We felt relaxed and comfortable sitting on the terraces and talking to people in a way that we didn't in Barcelona or San Sebastian. As a Spanish teacher, I also liked practicing the language without a lot of tourists speaking English. Of course the language is Basque, but it was fun to hear it spoken. I guess it depends on what you want to do and how long you are going to stay in a place. I loved Lekeitio, but I'm not sure if I would return there again. There are lots of places I'd like to visit in Spain.