Partial penetration welds and intermittant welds are both prohibited under fatigue loading. (See section 12.4.14 of W59, and I am sure AWS D1.1 has similar provisions.)
The only problem is that sometimes partial penetration welds are unavoidable. For example, how can you make a flare bevel weld that isn't partial penetration. I am not sure how you can comply with the code in a situation like this.
The design code for structures that I have been exposed to, that has great guidelines for handling fatigue loading, is BS 8118. This is however aimed at Aluminium. The equivalent for steel, I believe, is BS 7608.
What is great about this code is that you can take your weld detail, and by comparing it to some sketches, you can calculate a final fatigue life. Therefore, by changing your weld detail you can see how it affects your fatigue life. This is a slightly different approach to that taken by codes such as D1.1 (I am no expert on this code) which merely allows or disallows certain weld details.
Hope this helps.
Regards
Niekie Jooste