Since the whole TM6 thing when entering Thailand has been abandoned a few weeks ago, do we need to have new TM87 forms when applying for a Non-O, or is it acceptable to immigration to use the old forms and simply leave the section pertaining to TM6 empty? 

Not having a TM6 arrival card does not change the form need to a apply for non-o visa at immigration.

The TM87 form is used if you are on a visa exempt entry and the TM86 form is used if you have a tourist visa entry.

You leave the TM6 number space blank when completing the form.