Your research? Sure! Beat that to death on your primary/secondary applications! But you really, really don’t need two honors theses (or any, really) to show this.
I knew someone from my undergrad who did that in chemistry and in one of the biological sciences - ended up at a State medical school (like me, who completed no honors theses), so I doubt it mattered much.
Don’t do two honors theses. Writing one will be time consuming enough. You are better off devoting your efforts entirely to one project and squeezing the full potential out of that project and your work.