Most fighter jets don't leave trail in dry thrust.... Again, stealth & supercruise must go together.
I don't know who is feeding you wrong information about con-trail !!
Contrail is not associated with supersonic flight alone & the use of after burner in particular. You may see it even for M==0.85-0.9 at cruising altitude for civilian aircraft; Check this picture; Airbus 340 at cruising altitude(30-35k feet); I hope civilian turbofans engines doesn't use wet thrust !!
F-16 with contrails
For BVR engagement at cruising altitudes (for which most of the fighter jet have claimed supercruise capabilities), the visual confirmation via contrails plays an important part in highly cluttered environment. That's what the "FSO" of Rafale is supposed to do that; to visual ID the bogey at longer distance. Check out the extent of contrail left behind by fighter jets doing combat maneuvering (F15s intercepting a pair of Migs).
Picture courtesy : Wikipedia/Google
Subsonic jet will be heard before it reaches & he'll easily make visual contact then... But a sudden sonicboom echoing all over the place is more jarring as well as don't give away a direction.
So the time difference in which he can relay the info, say 2-3 minutes.
Even if the enemy responds within another 5 minutes (near impossible), you have released your ordnamce & turn to return home.
True; but then this scenario comes only when you are fighting war with sub-saharan countries with technologies dating back to WWI.
So far, the only aircraft with internal weapon bay that can supercruise and drop the ordinances is F-22 (in active service; not sure about J-20); even for that I would say going sonic over enemy territory is counter productive for strike missions unless you are just trying to intimidate them. Sonic boom can affect larger area around its passage rather than the sub-sonic flight meaning you are alerting larger number of people about its presence. From my perspective, significant utility of going sonic is in high speed interdiction; BVR combats, and defensive maneuvering.
There is a reason to the decline of usage of high altitude & high speed Mig 25 due to arrival of advanced EW radars and longer range SAMs.