and would like to upgrade the subwoofer however the sub in this system is marked as 3ohm. Now in car audio i could use a 4ohm sub and it would just get less power, which in most cases is fine you just need to adjust the building of the enclosure. Is it the same premise in home audio? I certainly don't want to run lower ohm being its a cheap HTiB and I'm sure running anything below rated will throw it into protect mode.
If using a new subwoofer driver that is 4 ohms, and assuming your previous one was 3, then your amplifier will power it just fine, but just put out a little less power as you know.
You'll want to build a new enclosure for the new driver.