Q:

Are there "transparent" clouds?

Comments below this answer to the question Why are lightning towers at launch pads topped with big hollow tubes with spiral windings and not “lightning rod-shaped” lightning rods? link to a 2013 Kennedy Space Center News item RELEASE : 13-03 Space Shuttle Weather Launch Commit Criteria and KSC End of Mission Weather Landing Criteria. It's quite detailed, and discusses cloud transparency in several places. 
Question: Are there "transparent" clouds? Are there any standards by which cloud transparency is measured or even visually quantified? I'm wondering if this is a Kennedy Space Center-specific term and they have their own way of estimating cloud transparency, or if it might be a standard meteorological term. Since launches can happen day or night, it calls into question how transparency is determined at night, and if it uses visible light or infrared measurements from ground or satellite.

Here are the most relevant excerpts in case the link breaks at some point in the future. This is from 2003.
There is one instance of "transparent cloud":

The one-minute average of the electric field mill network may not exceed -1 or +1 kilovolt per meter within five nautical miles of the launch pad or the lightning flash at any time within 15 minutes prior to launch. This field mill criteria becomes -1.5 or + 1.5 kilovolts per meter if there are no clouds within 10 nautical miles of the flight path except those which are transparent. Also excepted are clouds with tops below the 41 degrees F. temperature level that have not have been previously associated with a thunderstorm, or associated with convective clouds having tops above the 14 degrees F. temperature level during the last three hours. 

as well as a whole section on non-transparent clouds and parts of clouds:

Clouds: (types known to contain hazardous electric fields)
[...]

Do not launch if the flight path is through any non-transparent clouds that extend to altitudes at or above the 32 degrees F. level which are associated with disturbed weather producing moderate or greater precipitation, or melting precipitation, within five nautical miles of the flight path.
Do not launch through an attached anvil cloud. If lightning occurs in the anvil or the associated main cloud, do not launch within 10 nautical miles for the first 30 minutes after lightning is observed, or within 5 nautical miles from 30 minutes to 3 hours after lightning is observed. 
Do not launch if the flight path will carry the vehicle:
a) through non-transparent parts of a detached anvil for the first three hours after the anvil detaches from the parent cloud, or the first four hours after the last lightning occurs in the detached anvil.
b)  10 nautical miles of non-transparent parts of a detached anvil for the first thirty minutes after the time of the last lightning in the parent or anvil cloud before detachment, or the detached anvil after its detachment.
c) within 5 nautical miles of non-transparent parts of a detached anvil for the first three hours after the time of the last lightning in the parent or anvil cloud before detachment, or the detached anvil after detachment, unless there is a field mill within 5 nautical miles of the detached anvil reading less than 1,000 volts per meter for the last 15 minutes and a maximum radar returns from any part of the detached anvil within 5 nautical miles of the flight path have been less than 10 dBZ on radar (light rain) for 15 minutes. 
Do not launch if the flight path will carry the vehicle through a thunderstorm or cumulonimbus debris cloud which is not transparent and less than three hours old. Launch may not occur within five nautical miles of these debris clouds unless: 1) for 15 minutes preceding launch there is at least one working field mill within five nautical miles of the debris cloud; 2) all electric field mill readings are between -1 kilovolt and + 1 kilovolt per meter within five nautical miles of the flight path; 3) no precipitation has been detected in the debris cloud (less than 10 dbz by radar) within 5 nautical miles of the flight path. 

A:

Are there "transparent" clouds?

Yes.  One type is called subvisible cirrus clouds.  They're essentially clouds that are very, very thin.
According to Reverdy et al. (2012):

Spaceborne lidar observations have recently revealed a previously undetected significant population of Subvisible Cirrus (SVC). We show them to be colder than −74 °, with an optical depth below 0.0015 on average. The formation and persistence over time of this new cloud population could be related to several atmospheric phenomena. In this paper, we investigate if these clouds follow the same formation mechanisms as the general tropical cirrus population (including convection and in-situ ice nucleation), or if specific nucleation sites and trace species play a role in their formation.

As for your second question:  

Are there any standards by which cloud transparency is measured or even visually quantified?

According to Spreitzer et al. (2017), subvisible cirrus may be defined as cirrus with an optical depth of less than 0.03.
References
Reverdy, M., Noel, V., Chepfer, H., and Legras, B.: On the origin of subvisible cirrus clouds in the tropical upper troposphere, Atmos. Chem. Phys., 12, 12081-12101, https://doi.org/10.5194/acp-12-12081-2012, 2012. 
Spreitzer, E. J., Marschalik, M. P., and Spichtinger, P.: Subvisible cirrus clouds – a dynamical system approach, Nonlin. Processes Geophys., 24, 307-328, https://doi.org/10.5194/npg-24-307-2017, 2017.

