Yes, D trains are available from Wenzhou to Ningbo and also from Ningbo to Shanghai. I picked up the direct departure trains with timetable for you.

Wenzhou-Ningbo:
D5558 07:45/09:22
D5572 12:59/14:32
D5554 13:51/15:12
D5552 17:28/19:01
D5556 18:20/19:53

Ningbo-Shanghai:
D5582 07:15/10:35
D5584 14:41/17:38

hello, Mr.Saurabh. There are many D trains from Wenzhou to Ningbo and from Ningbo to Shanghai. Both morning and afternoon ones are available. You may choose as per your schedule. Here i pick each one of them just for your reference.
Wenzhou/ Ningbo D5572 1259/1432
Ningbo/ Shanghai D5552 1903/2217
BTW, there is D train from Wenzhou to Shanghai directly, see Wenzhou/ Shanghai D5554 1351/1512.
Hope it helps.

Ms Jenny, Can you tell me website for checking trains in between two places in english. Since wenzhou to ningbo is still not updated on travel china guide website.