Normally WRC-297 is to be used to ascertain nozzle flexibilities for cylinderical shells.But is it OK to use it for nozzles on the shell heads with vessel axis reoriented in the input model to have nozzle and vessel in perpendicular direction?
Actually using WRC-297 on shell head nozzles won't provide much flixibility but is it totally prohibited to use WRC-297 for shell head nozzles?
Looking forward to replies.

Thanks.

WRC-297 does not address the flexibilities of nozzles on heads. This type of configuration is outside the scope of this particular bulletin.

Implementing WRC-297 in this situation anyway (by specifying the orientation 90 deg from reality) means you are making assumptions, but it is the only way to get WRC-297 to work. If you do this, make sure you document everything so reviewers and owners know what you did.

Your alternatives are PD-5500 and/or Finite Element analysis.