The Stimulant Connection
Sudafed contains Pseudoephedrine, an active ingredient that can be chemically altered to produce methamphetamine. Because of this, Japan classifies it under its strict Stimulants Control Law.
Consequences
If caught with Sudafed at the airport, you may be detained, interrogated, and deported. It does not matter if it was for a runny nose.
Safe Alternatives
Look for cold medicines that use Phenylephrine instead, or buy local remedies in Japan once you arrive (ask for "Kaze-gusuri"). Medications containing Dextromethorphan are generally safe in normal quantities.