What I'm trying to understand is whether they were literally sailing into uncharted waters, or perhaps had some advantage from maps or crew captured from the Spanish, Portuguese, Dutch. And also, if other nations maybe had all the best African harbours, so English fleets were at a bigger risk that way too. Or was the hazard fairly uniform for any nationality who attempted it? Thanks for any insight.
The British East India company had a monopoly on trade between Britain and the Indies from 1600 to 1813 (when the monopoly ended except for tea, which continued until 1834).
During this period of over 200 years, there were about 4600 individual ship sailings from London to the East Indies (and, presumably, about the same number on the reverse voyage).
About 5% of these sailings ended in the loss of the ship.
http://jds.cass.cn/Item/5607.aspx
I don't know if earlier voyages had higher loss rates than later ones (working on my your hypothesis that losses might have been higher when English seamen were less familiar with the waters).
A quick glance at East India voyage records indicates that times of war caused increased losses through enemy or privateer action.
You could check on losses by date, as this source:
http://www.eicships.info/voyages/lostships/lostshiplistA.asp
gives all East India Company losses from 1600 -1834. Unfortunately the losses are organized alphabetically by the name of the ship, rather than by date, so it would take some statistical effort to recut the data to see loss trends by time period.