As someone who has done both, I think both schools of thought have their merits. (Author's Note: While in the US, Mother's Day takes place in May, I don't think the fact that we celebrate on a different date is cogent to my argument, although if you can think of a reason it is, please let me know.)
For one, handmade gifts have that personal touch.
I've crafted a lot of things for my mother for various holidays, including a polymer clay pendant of our dog's face, clay earrings from a primary school project and, as a very small child, pipe-cleaner bracelets. Given my level of artistic ability (i.e., not good enough for Etsy but better than I used to be), these gifts have been a hit. I have also made nice things for other family members that received positive reception, such as a blue heart-shaped clay pendant for my grandmother and a cardboard bird model from the craft store painted to resemble the varied thrush from the "Twin Peaks" intro for my father's desk.
Storebought gifts have charm as well. For instance, last Mother's Day I ordered two notebooks from Etsy for my mother, one with a fox design and one with bunnies, because I know that she likes journaling and loves woodland animals. I have also gotten her books about specific topics she is interested in, like birds. Since these gifts show my mother that I know what she is interested in, and are also things that she can and will use, I don't see them being less personal than homemade gifts. If I went out of my way to get something flashy and expensive without considering her interests, I think that would be disingenuous and take some of the meaning away, but that really isn't the case here.
Overall, whether homemade or store-bought depends on what you are getting. Is it a pre-existing piece of media or something that's already designed well, like a piece of jewelry or something with a nice pattern on it? Then store-bought is great! But if there's a creative touch to the item you have in mind that only you can bring to the table, go for the homemade route--even if you are not confident in your creative skills, your mum will appreciate a one-of-a-kind work of art.