I really feel embarrassed to ask this but... Basically I have an easy to trigger stomach and sometimes I get diarrhea and/or stomachache in the morning. And this wouldnt be an issue in the old days if the Masses are nearby or at least I could stop in the middle of the trip to use the loo. However, for me it's 3hr trip by myself with hardly anywhere to stop in the middle until I get to the spot and I feel that is too mentally draining for travelling with this condition. Yet I feel bad for missing Mass for a seemingly minor issue like this because I assumed to miss Mass for health reason it has to be something more serious. What do you think? Is it a justifiable reason to miss Sunday Mass for the travel time or sickness like this?

15 decades of The Rosary would be another way of meeting your obligation in your case

Sometimes I have a similar problem.  I also drive 3-3.5 hrs and try to attend once per month.  Like FarmerWife,  Often I don’t go in winter because of dangerous road conditions.  I’m older, so have no baby to care for.  Staying in a motel is expensive, and I have to save up gas and toll money for the monthly trip.
It may sound a bit “off,” but the larger part of my drive is on rural roads.  If I have an emergency, I make a dash into the woods to “visit Mrs. Murphy,” as we called it on family road trips when I was a youngster.  Just be neat, if TP is used, be sure to bury it well or bring it back in a container to be disposed of later.  Depending upon the situation, you may be able to use tree leaves or moss.  Carry with you in your vehicle, hand sanitizer, wet wipes, or just a jar with water, soap, a little bleach.  Splash a little on your hands.  In the days before conveniences like today, that’s what we did. 

Impossibility or serious inconvenience excuses from hearing Mass (e.g., those who have to walk an hour's journey to church or ride a two hours' journey, regarding which, in terms of distance travelled, it has been suggested that the figures should be more than three miles each way if one must walk, more than thirty miles if a car is available and the roads are good; those who will suffer great detriment to health, honor, fortune, etc., if they go; those who are kept away by duties of charity or employment or office that cannot be omitted).
Necessity or duty to others permits one to work on Sunday at least to some extent (e.g., those who must labor on a Sunday in order to live, or to keep out of serious trouble, or to perform services or works of charity that cannot easily be done at another time).
To avoid self-deception the faithful should consult their pastor or other prudent person if there is doubt about the sufficiency of the excuse.

This is a bit extreme, but you could do a bucket and bag if you needed to do a number 2. And then dispose of it in the trash. I know an older couple took their RV so they can have easy access to a bathroom.