Initiative rolls do not generate hits, so how are the dice pool modifiers from sustained spells subtracted?
There are no rules stating that there is any effect on initiative so there is none.
Core Rulebook, p. 282
If you sustain the spell [...], you take a -2 dice pool penalty to all tests while it is sustained.
Sustained spells don't affect initiative. You don't use a dice pool for initiative and it's not a test either.
You can act just as fast while sustaining spells but if you do anything that requires a test, you're less effective.
Similarly your base carrying capacity is not affected, but if you want to carry more doing a \$BOD + STR\$ test, you'd suffer the negative effects of sustaining spells for this test.