SeaWorld San Diego’s Penguin Encounter is still there.
The official site currently lists five penguin species: king penguins, Adélie penguins, gentoo penguins, chinstrap penguins, and macaroni penguins. The exhibit also has a Penguin Cam, which suggests it is not just a historical page.
This is also where San Diego differs from SeaWorld Orlando. Orlando now pushes emperor penguins and Penguin Trek forward; San Diego keeps a setup closer to the classic cold-room bird house.

What to see
The official site notes that from May to July, Penguin Encounter simulates Antarctic winter, so the light level is very low and fill light and flash are prohibited. That is not fine print, because light directly affects the birds’ physiological rhythm.
When viewing, start with size differences. King penguins are the tallest; Adélies and chinstraps are smaller; macaroni penguins have yellow crests on the sides of the head. For underwater speed, you have to wait until they decide to swim. That is when the exhibit’s real value appears.
To separate the two San Diego routes, pair this page with San Diego Zoo. One is a cold-water group; the other is an African coast.

How to plan it
Regular admission lets you see Penguin Encounter. Ultimate On-Ice Penguin Experience is an add-on if you want to step onto the ice. It is expensive, limited, and has clearer height and mobility rules.
Penguins Up-Close Tour is shorter and centers on keeper interpretation and close observation. For both experiences, do not judge only by price; check whether your group can handle the cold and restrictions.
If you are organizing a global zoo route, return to the penguin zoo overview to compare the North American representative sites.

Penchan Says
SeaWorld San Diego is not a smaller version of Orlando.
It feels more like an old-school but still working penguin specialist exhibit: light, temperature, mixed species, and husbandry limits are all visible.
References
FAQ
Which penguins are in SeaWorld San Diego Penguin Encounter?
The official site currently lists king, Adélie, gentoo, chinstrap, and macaroni penguins.
Why is the exhibit dark from May to July?
SeaWorld notes that Penguin Encounter simulates Antarctic winter during that period, so light is very low and fill light or flash is prohibited.
Can regular admission see Penguin Encounter?
Yes. Regular admission lets you see Penguin Encounter; on-ice and up-close experiences are add-ons with availability and access limits.