Hoechst, no but I have been using DAPI in PBS for a long time.

Overall I would say, that you should not worry about washing the signals away afterwards, as long as they are performed at room temperature on formalin fixed tissue. Several protocols uses indirect detection of ISH signals, fx using Digoxigenin labelled probes that are then detected using antibodies. These protocols involve several washes following stringency wash, without giving rise to problems.

When the hybridization has occured, the signal is quite robust.

I stain with Hoechst for 5 mins in the dark after post-hybridisation washes and it is always fine