Although both forms refer to a repeated, regular action, the use of "having to" indicates that the action is due to need or requirement. If you need more information please let me know.

To understand better, let's look instead at simpler sentences that display the same structure: "It is fun to swim." "It is fun swimming." Present participles and infinitives both can function as nouns. In these sentences, "to swim" and "swimming" are both nouns and serve the exact same grammatical role in both. The only difference is that they feel different. Infinitives feel factual, whereas present participles feel descriptive. These nouns, "to swim" and "swimming", specify the meaning of "it". Really, "it" is superfluous in these sentences. The sentences are better without that word: "To swim is fun." "Swimming is fun." Likewise, your sentence is better without "it": "Not having to drop off and pick up my kids every day from separate day cares is great."

In the sentence "It's a big perk and it's great not having to drop off and pick up my kids from a separate daycare every day," the use of the gerund ("having") after "great" is a stylistic choice. Both versions of the sentence are grammatically correct, but they convey slightly different nuances. Using the gerund emphasizes the ongoing action or experience of not having to drop off and pick up the kids from daycare. It implies that the speaker is currently experiencing the benefits of not needing to do these tasks repeatedly. On the other hand, using the infinitive ("not to have to") focuses more on the absence of the need to perform the action. It suggests a general state of relief or satisfaction with the situation. In essence, both versions are valid, but the choice between gerund and infinitive can depend on the writer's preference for emphasizing the ongoing nature of the action or the absence of the need to perform it.

Being able to drop off (all) my kids at the same daycare (everyday) is a big perk. It’s great being able to use just one daycare.

Both sound natural, there’s no way to know why the author chose one over the other. It could be a regional preference.