Actually you can connect to a an SSL-encrypted connection with dplyr
and it's easy.
You just need to pass the parameters for your connection within the dbname
parameter, like this (this is a postgresql example):
db <- src_postgres(dbname="dbname=my_db sslcert=my_cert.crt sslkey=my_key.key sslmode=require", user="username", host="your.host.com")