The British Horseracing Authority "robustly condemned" the protests, adding it would analyse the races to understand what caused three horse fatalities at the meet.
BHA chief executive Julie Harrington told BBC Sport a "direct parallel" between the interruption and the horse's death could not be drawn, but added: "I will say it certainly cannot have helped".
"Whilst the horses are running, if they're disturbed in any way, it is a really dangerous thing, so we would condemn that action."
Footage appeared to show some protesters making it on to the track and trying to attach themselves to a fence, before being removed by police.
Dozens of others attempted to climb over or glue themselves to security fencing around the track but were led away, with police also confiscating ladders.
After the delay was announced on the racecourse public address system, the 39 participating horses were taken back to the pre-parade ring.
The jockeys were asked to re-mount their rides six minutes after the scheduled start time, with the race starting eight minutes later.
Thomson added that Hill Sixteen was "quite used to the fences" at Aintree having previously finished second in the 2021 Becher Chase and seventh in this season's version of the same race.
As well as the death of Hill Sixteen, Dark Raven was put down earlier on Saturday following a fall during the Turners Mersey Novices' Hurdle, while Envoye Special suffered a fatal injury in the Foxhunters' Chase on Thursday.
There have been five fatalities from 395 runners in the 10 Grand Nationals raced since safety changes were introduced in 2012.
"Nobody wants that to happen to their horse but that is what they are bred to do, what they love doing. They wouldn't jump these fences if they didn't want to," Thomson said.
Two other horses in the Grand National - Recite A Prayer and Cape Gentleman - were treated on course and taken away by horse ambulance for further assessment.
Trainer Willie Mullins told Racing TV, external that Recite A Prayer will be fine following a "little procedure" on a fractured eye socket sustained when running loose after jockey Jack Foley was knocked off.
Trainer John 'Shark' Hanlon said Cape Gentleman had surgery on Sunday for a severed tendon and will head to the United States to spend his retirement with owner Pierre Manigault.
Thomson said the number of horses falling in the race "point to the fact" they were unsettled by the delay.
"If we look at the last nine years since the course has been modified there's been an average of under two fallers at the first two fences," he said.
"This year everyone got very uptight about it - horses, jockeys - and there were eight fallers at those first two fences.
"We as a sport are continually moving forward, we're continually trying to make the sport safer."
ncG1vNJzZmivp6x7o67CZ5qopV%2BovbC%2B02ifqKqjmnqzrcKipaBnZmp%2FeoKVcmo%3D