Desertion was quite common even before the soldiers were embarked at Chester or Bristol. Both cities suffered mass desertion and mutinies from troops awaiting transport and the mayors of those cities repeatedly petitioned Elizabeth for martial law to be imposed on the areas (it never was). Troops also slipped away from their conductors en route – and as the conductors or their aristocratic bosses were contractually obliged to turn up with a certain number of men to collect their cash, they impressed any beggar, criminal or vagabond on their route to the ports to make up the numbers. These groups of ‘soldiers’ were rarely the most committed of men and whilst happy to get away from whatever trouble they were in in their home area, saw no need to actually go all the way to Ireland and fight.
As OB said, once in Ireland there were opportunities to return without getting involved in any of that messy fighting business, although it was more difficult.