How do bakeries get smooth jam to top their cheesecakes with?

You are thinking of jelly like actual jelly in a can: Sweetened fruit juice thickened with pectin. While some bakeries use special pectin to make glazes (look at LM pectins) most jelly fillings and glazes are made with starch. In the US, usually corn starch.

Jelly donut filling is like canned pie filling: a sugar syrup that is thickened with starch. This is an example recipe.

Fruit glaze toppings are similar but have a bit more starch so they set up more firm. Here is a commercial example. Notice the ingredients, corn syrup and corn starch are prominent.

Starch is cheap, sets up firm and is less sweet than sugar. Pectin has a better texture and flavor, in my opinion. When making glazes at home, boiling down jams and jellies produces superior results.

I haven't actually tried this on a cheesecake specifically but, when I need a spreadable jelly, I'll heat it in a pot until it goes back to being a runny liquid. (It's original state before the starch/pectin cooled and gelatinized.) Let it cool slightly then pour it over whatever you want to cover.

The topping for the cheesecake in my profile picture wasn't a jam but instead a very thick coulis made with puréed, strained blueberries and arrowroot (starch). I added some whole blueberries back in on this one, but you get a very smooth shiny topping if you don't do that. This is then quite stable.

To quote the wikipedia page linked above:

Arrowroot makes clear, shimmering fruit gels and prevents ice crystals from forming in homemade ice cream. It can also be used as a thickener for acidic foods, such as Asian sweet and sour sauce. It is used in cooking to produce a clear, thickened sauce, such as a fruit sauce. It will not make the sauce go cloudy, like cornstarch, flour, or other starchy thickening agents would. _{Emphasis mine}

Put some sugar in a saucepan on super-low heat and add pectin right before it's caramelized, add a water/neutral vinegar/lemon juice mix, then put in macerated strawberries and cook down until almost before syrup. If you run that through a chinois (shinwah) and add cornstarch you'll get that effect. I would also try making a loose strawberry "curd" and finishing it with cornstarch.

It's most likely flavoured jelly and not jam.

Here is an example recipe of cheesecake with strawberry jelly, I haven't tried the recipe myself so I don't know if it's any good.

To make smooth jam topping for my cheesecakes or other baked goods, I use a stick blender, food processor or blender with a tablespoon or so of hot water and a jar of jam or preserves and process to the consistency I want.