One way to get rid off the warnings is to manually tell sbt what dependencies you prefer, for your case:
dependencyOverrides ++= Set(
"io.netty" % "netty" % "3.9.9.Final",
"commons-net" % "commons-net" % "2.2",
"com.google.guava" % "guava" % "11.0.2"
You can also read about conflict management in sbt.
Should I care about warnings at all?
In your case I would say no, since your conflicts stem from using only spark-related artifacts released under same version. Spark is a project with big userbase and possibility of jar hell introduced due to transitive dependencies is rather low (although, technically not guaranteed).