When bolting something like a flange or a dead/blind end to a port on a pressure vessel (lets say rated to 2 ATM), is there a good rule of thumb on how much of the threading should be engaged into the tapped hole in the vessel?
Is there an ISO standard or something and if so can someone provide a reference to the standard?
When dealing with pressure vessels, you should not rely on rules of thumb. You should rely instead on the ASME Boiler and Pressure Vessel Code or whatever code is required by your local enforcement or regulatory body.
There are far too many variables for a one-size-fits-all answer. The design pressure/temperature, materials of construction, flange configuration, gasket material, etc all play a role.
Bolts are not typically used for these types of connections. Instead you would install a threaded stud in the vessel and then use a washer and nut to hold the flange.
Section VIII Division 1 UG-43 states that a tapped hole for a stud shall engage the stud for a length not less than the larger of $d_s$ (the nominal stud diameter) or $$0.75d_s \times \Big( \frac {maximum \space allowable \space stress \space value \space of \space stud \space material \space at \space design \space temp}{maximum \space allowable \space stress \space value \space of \space tapped\space material \space at \space design \space temp} \Big)$$
except that the thread engagement need not exceed 1.5$d_s$.
I have always used the rule of thumb that the bolt has to be engaged at least one bolt diameter.
This partly comes from looking at structural nuts. Structural nuts develop the full strength of the bolt in tension. These nuts typically engage about one bolt diameter.
