I work very closely with an NGO, and know how much donations by the general public are needed and appreciated. However, I suggest you simply make the donation without mentioning it to your guests.
First, I believe it is fundamentally wrong to push a cause on another person. And that is essentially what you are doing with the "in honor of". Someone will think "Why a donation to a hospital when there are children in this world who cannot attend school?" Cruel, but someone will think it. On the other hand, if you give to UNICEF someone will grumble about the lack of efficiency, wasted funds on fancy buildings and glossy image-building, and endless red tape and paperwork in the organization. You cant please everyone -- even for a good cause!
Second, it may come across as showy and bragging. I know firsthand that those who announce donations or look for recognition often do NOT make good on their promises.
Third, favors are going out of style and your guests will not miss a candle one bit. In fact they will probably not even notice that there are no favors. So, you do not owe them a favor, nor do you owe them an explanation of where that "favor money" went to.
Fourth, if your guests want to donate to the animal shelter.... believe me, they will. You dont need to do it for them.
And fifth, your wedding is not the time or the place for charitable solicitation, advertising, or otherwise. Make that donation! Just dont make it be a part of your wedding. Its just not in good taste. Peace.