Smoke grenades can be circumvented in a number of ways: heat vision (e.g. Swarmids, Chasers, Floaters, Meridian
); sniper-spotter tactics (many an enemy can shoot outside their vision range), height (explosions are not spheres, they have less height than width), or just not having enough smoke between you and an enemy.
Ninjas are actually visually indistinguishable from BL Warriors, who do not have their stealth powers. So if you can see a 'ninja', chances are, it's not one.
Bughunt mechanics are described
here. For XCF, the thresholds are 3 enemies, 20 turns, commanders disable bughunt, the morale check is either disabled or 0 morale (i.e. close to impossible to achieve), the 'stuck' threshold is 65% of TU. Notice that there is a 'no visible enemies' requirement, too!
Yes, accuracy does not count for non-vision-obscuring obstacles. The enemy can have only a small sliver visible at the edge of some apple tree, and the game will report high accuracy while the soldier will miss and miss and miss...
There are several different types of covert missions, and most equipment has filters for that ('Concealable', 'Beach gear', 'Labour gear', etc) in equipment screens (craft, buy). When
you click on a mission marker on the globe, the game tells you which armours are allowed. UNARMORED (DOG) (and not un
armed!) means no armour, or it will be downgraded to UNARMORED (DOG).