How is the site of administration of a vaccine decided?
When the effectiveness of subcutaneous is comparable to intramuscular, then the choice is made based on the degree of discomfort and adverse reactions.

In many situations intramuscular will outperform subcutaneous delivery due to subcutaneous fat having poor vascularity which may result in slow mobilisation and processing of antigen(source).

Disclosure: I am not a biologist so this is outside my field of expertise.