Using Apple Watch to track your health and fitness activities is great, unless the companion app you rely on doesn't log your heart rate—and that means any third party app. As annoying as that is, there's a real reason behind Apple's decision, and it isn't one they'll likely change soon.
HealthKit encryption on your iPhone means no heart rate tracking for Apple Watch apps
Third party apps can't access HealthKit data when your iPhone is locked because it's encrypted. That encryption prevents third party apps from passing data through HealthKit, which ultimately means features like heart rate tracking—at least for now—is off limits.
Apple's HealthKit encryption system is keeping some companies from releasing Apple Watch-compatible versions of their apps, including Flask and their FitPort app. That's a shame because FitPort is substantially more useful than Apple's own Health app.
Some app developers decided to roll out apps that offer fitness tracking without heart rate even though they seem feature hobbled. Maybe Apple will change how HealthKit data is handled at some point to make it possible for third party developers to take full advantage of Apple Watch's built-in heart rate sensor, but for now it looks like how heart rate data is logged is going to stay very limited.