Let's compare them.
50 Base power(25 each)
Can Poison Steel and Poison types..
Has 100% accuracy
14 Base power each(possibly 70 if all 5 hit)
No additional effects
Has 85% accuracy
Twineedle is far better, the only time Pin missile is superior is if it manages to hit 4/5 times, which is very unlikely.
Twineedle also has a 20% chance to poison the target each hit and as a bonus can even poison Steel and poison types.
Not to mention it's 100% accurate, unlike Pin missiles 85%