In the GLAS altimetry products, is there an indicator to the presence of clouds?

Yes, it is an element of GLAH06, GLAH12, GLAH13, GLAH14, and GLAH15. 

The Multiple Scattering Warning Flag, cld1_mswf_flg, is based on the total column optical depth (aerosol plus cloud) calculated in GLAH11 using 532nm. It is intended as a way to quickly obtain information about the potential severity of multiple scattering with regards to the range-to-surface calculated by the altimetry processing software.The multiple scattering warning flag will have values ranging from 0-14, based on the total column optical depth. A warning flag value of 15 will signify 'invalid'. An invalid will be encoded if an optical depth in any of the layers in the 1-second column could not be calculated. This usually occurs in a very optically 'thick' cloud which extinguishes the signal. It could also occur if the extinction-to-backscatter ratio assignment is set too high, causing the transmission calculations in the lidar inversion to go out-of-range.

The Medium Resolution Cloud Availability Flag, MRC_af_flg, tells how many cloud layers were found at this resolution from the 532 nm channel.

The Full Resolution 1064 Cloud Top, d_FRir_cldtop, parameter is the full resolution (40 Hz) cloud top height obtained from the 1064 atmospheric channel. This parameter is for a 1 second record.