It's not like China would just invade the country at a whim, that would damage the reputation it is trying to build up, not to mention that would alert all the other claimants. There is also the defense treaty with the US. China wants the US out of the region, China attacking the Philippines would draw the Americans in with the reason as "defending a long-standing ally". Even without the treaty, I'd imagine they'll go hostile and support a proxy war in the Philippines to drive out the Chinese.

This is why the Chinese Navy don't send their ships there but rather the Coast Guard which is considered more "civilian". If they send the Navy people would cry out "invasion!". With the Coast Guards, China would just say they are patrolling "their" territory, disputed it may be.

As for the shipping boats, they've already done that. People call it "the cabbage". Surround the area with fishing boats, then later coast guard ships "escorting" the earlier boats, and before you know it, they're dumping sand on the reef.