...So, which excuse do we make for such missile strikes never being in evidence?
- There exists a defense?
- Bushido rules?
- Nobody wants to destroy a planet if one can conquer it?
- Strikes take place but we don't discuss it with outsiders?
I don't think any of these would be much affected by the introduction of phase-cloak technology. Countermeasures against classic cloaks are haphazard at best already, and the other snappy answers aren't technology-related.