For me, it certainly makes a lot of sense to have a statue of Dorje Shugden on the shrine/altar. Dorje Shugden is much more than a mere Dharma Protector even though he is in fact the King of Dharma Protectors. He is in fact, first and foremost none other than Manjushri Je Tsongkhapa and therefore the very statue of Dorje Shugden is a very apt representation of all that Je Tsongkhapa embodies which are in essence, are Manjushri, Avalokiteshvara and Vajrapani.
Just by looking at the statue of Dorje Shugden we see that his form itself reveals the complete stages of the path of Sutra and Tantra, and these qualities are not possessed by the forms of worldly beings and only by fully enlightened Buddhas.
Dorje Shugden attire represents a fully ordained monk to show that the practice of pure moral discipline is essential for those who wish to attain enlightenment. In his left hand he holds a heart, which indicates his great compassion and spontaneous great bliss – the essence of all the stages of the vast path of Sutra and Tantra. His dome hat represents the correct view of Emptiness necessary to gain enlightenment, and the wisdom sword in his right hand teaches us to sever ignorance, the root of samsara, with the sharp blade of Nagarjuna’s view. This is the essence of all the stages of the profound path of Sutra and Tantra.
Dorje Shugden rides a snow lion, the symbol of the four fearlessness of a Buddha, and has a jewel-spitting mongoose perched on his left arm, symbolizing his power to bestow wealth on those who put their trust in him. The single eye in the center of his forehead symbolizes his omniscient wisdom, which perceives directly and simultaneously all past, present, and future phenomena. His wrathful expression indicates that he destroys ignorance, the real enemy of all living beings, by blessing them with great wisdom; and also that he destroys the obstacles of pure Dharma practitioners.
Therefore it is adequate to have this single statue of Dorje Shugden on the shrine and this 7" statue of Dorje Shugden is so extremely beautiful and sacred.
Read about the significance of a shrine here too. Everyone should have this blessed statue:
http://www.dorjeshugden.com/all-articles/features/dharma-demystified-the-significance-of-a-buddhist-shrine/