Congratulations on your wedding!

To answer your question, your wife can apply for spouse visa even if her passport still shows her maiden name. From what I read in this forum, others were able to apply for spouse visa with just a marriage certificate issued by LCR. But for my case, I was asked to submit NSO marriage certificate so I requested for an early endorsement to NSO upon filing in Pasay LCR. It took me 3 weeks before I got a copy of my NSO marriage certicificate. You may want to check www.vfs-uk-ph.com to know more on spouse visa application (what are the required supporting documents). Or you can use the SEARCH facility in this forum to find the answers that you need because there are already a number of post made on spouse visa application.