It seems like the most popular nicknames for “Mary” are [name_f]Mae[/name_f] and [name_f]Molly[/name_f]. I’m not really feeling [name_f]Molly[/name_f] lol. How do I figure out if she should just go by [name_f]Mary[/name_f] or by [name_f]Mae[/name_f]? [name_u]Will[/name_u] she look like a [name_f]Mary[/name_f] or [name_f]Mae[/name_f]?
Other nicknames to consider?
[name_f]Mary[/name_f] [name_f]Katherine[/name_f] could be called [name_f]Mary[/name_f] [name_f]Kate[/name_f] which I find adorable!! 
I personally don’t think [name_f]Mary[/name_f] needs a nickname - none of the Mary’s I know use one, but it’s a pretty small sample size 
[name_f]Mae[/name_f] / [name_f]May[/name_f] and [name_f]Molly[/name_f] / [name_f]Mollie[/name_f] are nice, and although you can get them from [name_f]Mary[/name_f], it wouldn’t cross my mind intuitively.
Some more nicknames:
[name_f]Maisie[/name_f]
[name_f]Minnie[/name_f]
[name_f]Mimi[/name_f]
[name_f]Polly[/name_f]
[name_f]Missy[/name_f]
[name_f]Maire[/name_f]
What are your reasons for choosing [name_f]Mary[/name_f]? It’s a lovely name, one of my favourites, but I’m curious.
If it’s for Catholic reasons, there are plenty of other [name_u]Marian[/name_u] names/titles you could choose from that still honour [name_f]Mary[/name_f] but aren’t [name_f]Mary[/name_f], e.g. [name_f]Stella[/name_f] (Stella Maris)
Good luck! 
I think you’ll know if she’s a Mae or Mary - one will feel right 
Some other ideas for ‘Mary Katherine’:
Mack/Mak
Mimi
Airy
Ry
Ree
Mitzi
Mikki
Mika
(I mean, Merricat is an option, but is it the best association? Maybe not, but it could still be fun!)
You could just try to call her Mae sometimes and see if it sticks. If Mae doesn’t feel natural then she can go just go by Mary without a nickname.
You could also consider Mim, Mary-Kit, Marine, Matty, Marty or even Mickey.
May Kay?
Other ideas:
Maisie Rin
Mamie Kit
May Nené / Menené
Mattie
Maggie / Mackie / Mack
Maka
Marnie
Math
Ari Tay
Mitzi Kate / Mitzi Käthe (prn. Kete) / Mitzi Kete
Molly Kat
Manon
[name_f]Mary[/name_f] [name_f]Kate[/name_f] was my first thought (too [name_f]Mary[/name_f] [name_f]Kate[/name_f] and Ashley?)
[name_f]Mary[/name_f] K
I know of a little [name_f]Mary[/name_f] [name_f]Kate[/name_f] (that’s actually her name instead of [name_f]Mary[/name_f] Katherine) and she gets called MK a lot. It totally works and makes a sweet little nickname!
I second the nn MK!
Also, I love [name_u]Mars[/name_u] as a nickname for [name_f]Mary[/name_f].
I knew a [name_f]Mary[/name_f] [name_f]Katherine[/name_f] who went by MK!
[name_f]Mary[/name_f] [name_f]Kate[/name_f]
[name_f]Mary[/name_f] [name_u]Kay[/name_u]
[name_f]Mary[/name_f] [name_f]Kat[/name_f]
[name_f]Mare[/name_f] [name_f]Kat[/name_f]
MK
I’d probably call her [name_u]Kitty[/name_u]. I like MK too.
[name_u]Mako[/name_u] 
I second [name_u]Mako[/name_u]!
Maren/Marin?
[name_f]Myka[/name_f]
[name_u]Mack[/name_u]
Macky or [name_m]Mackie[/name_m]
[name_m]Kam[/name_m]
[name_u]Mar[/name_u]
[name_f]Marka[/name_f]
[name_f]Mikaela[/name_f]
[name_f]Mary[/name_f] K
[name_f]Mary[/name_f] [name_f]Kat[/name_f]
Mary-Kat
[name_f]Kat[/name_f]
[name_u]Kitty[/name_u]
[name_f]Mary[/name_f] [name_f]Katya[/name_f]
Mary-Katya
[name_u]Kay[/name_u]
[name_u]Kaye[/name_u]
[name_f]Maia[/name_f]
[name_f]Kaia[/name_f]
[name_f]Kata[/name_f]
[name_f]Kate[/name_f]
[name_f]Katie[/name_f]