Thank you for the question, Barb.
I would say yes. On a math worksheet, any equals sign needs to be in Nemeth Code. If there is an anchor before that equals sign and/or a link after it (even if both the anchor and link consist of nothing but words/letters), those need to be included in the switch indicators that are required for the equals sign.
This prevents us from either 1) using both the UEB equals symbol and the Nemeth equals symbol in the same document or 2) switching into Nemeth Code only for a sign of comparison while leaving its anchor or link outside in the cold.
Once you've used Nemeth Code for anything in a transcription, then the whole transcription should abide by the marriage of Braille Formats and Nemeth Code formatting rules.
Please do not hesitate to follow up here with any questions or worries you have about this.