GMT and joeboygo both offer good and interesting answers, but I'm going to take a slightly different stab at it.
The way Tomoe's face is consistently obstructed reminds me a lot of the character "Wilson" from the old TV sitcom "Home Improvement".
Wilson, in Home Improvement, typically served as a "voice of wisdom" that Tim would consistently get advice from when faced with difficult moral dilemmas or just tricky practical life problems. So I think that the idea behind obscuring Wilson's face was to emphasize this "larger than life" quality to Wilson and how he wasn't so much an active character in the show as he was like a mysterious sage who's there to guide Tim through difficult times in his life.
Much the same is true of Tomoe. Tomoe is there to help guide Houtarou through life, and get him to slowly but surely come out of his shell. She's not an active character in the show so much as she's a mysterious "larger than life" sage who's there to play a central role in Houtarou's character development.
Also, by not showing a character's face, the message becomes more important than the messenger. It ironically
adds weight to Tomoe's words.