Any suggestion that Thomas and Shaw were no-shows because the club did not want them there is completely false, according to the Magpies.
Thomas is expected to join Carlton through the free agency period next week, while Shaw and the Magpies have mutually agreed to explore other offers.
Shaw has already had a number of suitors, with Geelong, Essendon, Hawthorn, Greater Western Sydney and Melbourne among those interested in a trade.
AFL.com.au understands both Thomas and Shaw had conversations with club officials, during this week, who urged the pair to attend the count.
However, given the current climate, Thomas and Shaw felt it would be inappropriate to attend and ultimately decided to call in their absences.
Twitter: @AFL_BenGuthrie
