I don't know how airtight a standard baseball cube is. I suppose holes for ventilation couldn't hurt.
Biggest concerns after obtaining the autograph would be light/UV exposure, temperature, and humidity.
As for getting the autograph, you should always use a ROMLB baseball (anything else will cause the autograph to fade especially baseballs made from synthetic leather). I'd also just stick to using a high-quality blue ballpoint (like a Uni-ball Jetstream).
Some users on here have used a fine or small Staedtler Lumocolor in blue and it looks amazing. Pretty confident you'll never have fading issues.
India ink would probably work similar to the Staedtler but as you pointed out only seems to come in black.
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