Yarn and npm (version >=3.0.0) should be relatively compatible, especially moving from npm to Yarn, because compatibility is one of the stated goals of Yarn. As stated in Migrating from npm:
Yarn can consume the same package.json format as npm, and can install any package from the npm registry.
So, in theory, any package.json that is valid for npm should also work equally well for Yarn. Note that I say that npm v2 is probably less compatible – this is because npm migrated from a nested node_modules structure to a flat layout (which is what Yarn uses). That said, Yarn and npm v3 should produce very similar layouts, because, as stated in the issue I linked:
To a first approximation we should try to be very compatible with the node_modules layout for people who need that compatibility, because it’ll be the most likely way to avoid long-tail compatibility problems.
However, you will not be able to take advantage of the Yarn.lock generated by Yarn, because (as the name suggests) it’s only supported by Yarn, and npm shrinkwrap is not compatible.
Also, as noted by @RyanZim, older versions of Yarn don’t support pre- and post-install hooks, but versions later than v0.16.1 do. If you rely on these hooks, you will need to specify to users that versions greater than v0.16.1 are required.
In summary, as long as you encounter no bugs and only use features that are shared by both package managers, you should have no issues whatsoever.