I think you need to define by what you mean by "reinforced."

In B31.3 and CAESAR, the "reinforced" type is a hole cut into the header pipe, the end of another pipe trimmed to fit the hole, and then a reinforcement pad is added and all components welded together.

Edit to add: B31.3 and CAESAR absolutely do take into account repad thickness and diameter.

You may be referring to a different kind of "reinforced" tee, which may be just a welding tee, but is just thicker.

If this is the case, then I would recommend you place nodes at the ends of the tee, and increase the thickness and diameter of the tee, unless you know for certain there's more than adequate safety factor built in.

Not doing so would would be inaccurate, and will lead to some conservative AND non-conservative results. Yes, stresses in the tee will be overstated, but flexibility of the tee will also be overstated, as well, and resultant forces and moments everywhere else will likely be understated.

The degree by which these values are over/understated will depend on what fraction of the total system length these extra thick tees take up, and various aspect ratios of the system.