No, there are no temples dedicated to Vishvaksena where he is a main deity. In fact there won't be temples dedicated to him.
Vishvaksena presides over the obstacles and the army of Lord Vishnu. Vaishnavas and Vaikhanasas worship him before starting any ritual to remove obstacles. These follow Pancharatra and Vaikhanasa agamas respectively where Vishnu is said to be the supreme. Methods of his worship are given in these texts but not as main deity. It is instructed to construct a separate shrine for him. This is seen in major Vaishnava temples. Even though Vishvaksena (known as Vishwaksena Perumal) is the commander in chief of the army of Lord Vishnu and the removal of obstacles, he is still a servant to Lord Vishnu. He is one of the Nitya suris. These Nitya Suris are servants of Lord Vishnu. Similarly, he is seen as a servant of Lord Vishnu. Wherever there is a shrine to Vishwaksena, the main temple is of Vishnu (or his incarnations) only.
According to rules in Tirumala Tirupati temple (which follows Vaikhanasa Agamas), the flowers and garlands used for Lord are to be used for Garuda and Vishwaksena [Source- Video by Ramana Deekshitulu, former chief priest of Tirumal Tirupati Devasthanam (Telugu)]. Similarly, official website of TTD says the following about Vishwaksena temple in Tirumala:
Sri Vishvaksena Temple is located at the northern side of the main temple, in the Mukkoti Pradakshinam. Sri Vishwaksena occupies an important place in the Vaikhanasa Agama. In Vaishnavite functions and temple rituals, Sri Vishwaksena is worshipped first. Vishwaksena is said to be the chief of the army (of the Lord) and is believed to protect the function or ritual from evil. The idol of Vishwaksena and its worship are strictly in accordance with the Vaikhanasa Agama. During the daily worship of Lord Venkateswara, the garlands and flowers (called nirmalya) from the Lord's idol are removed and Vishwaksena is worshipped with them. Before commencement of the annual Brahmotsavam, the Senadhipathi or Vishvaksena Utsava is performed followed by Ankurarpana. His idol is also taken out in a procession during the Adhyayanotsavam.
This temple is near the main hundi. This is not open for devotees for a close darshan. We can only look at his idol from distance. There is another place in Tirumala itself. After having darshan, tirtha and shathari of Lord Venkateshwara is given to devotees. Along with Vishwaksena, small idols of Garuda, Ananta, Angada, Hanuman can also be seen here.
So, the role of Vishwaksena in a Vishnu temple is presiding over the obstacles and supervision of the rituals and puja done in the temple. This also means that Nitya Suris get satisfied with the worship of their master (Lord Vishnu).
Another reason is the relation between Paramatma and the Jiva. Sri Vaishnava tradition emphasizes on the relation of Shesha - Sheshi (Servant - Master). This is the most important relation among the nine relationships between Paramatma and Jiva (as stated by Pillai Lokacharya in Navavidha Sambandham). Hence, the Nitya Suris (who are also Jivas but of the highest category) do not consider themselves to be superior and always want to worship and serve the Lord. This is the reason why there is a separate shrine of Vishwaksena. Vishwaksena is known as both Vishwaksena Alwar as well as Vishwaksena Perumal. Alwar suffix is used when the servant aspect of his is talked about. Perumal suffix is added when he is worshipped as the commander of chief and removal of obstacles. Lord Vishnu approves whatever Vishwaksena Perumal suggests. That is the importance given to him by Lord Vishnu.
One may ask about Ganesha being the obstacle remover in Shaivite tradition but still having main temples dedicated to him. There is a reason for that also. Ganesha or Vinayaka is one of the five main deities in Hinduism. It means there were five main sects. They are
Shaivism (where Shiva is worshipped as supreme)
Vaishnavism (where Vishnu is worshipped as supreme)
Shaktism (where Shakti is worshipped as Supreme)
Ganapatyam (where Ganapati or Ganesha is worshipped as Supreme)
Sauram (Sun God is worshipped as supreme)
These were the five sects in the ancient times. Each have different set of worshipping methods and texts (agamas) dictating how to worship respective Lords through rituals and temples. Ganapatya sect also had a different set of Agamas called Ganapatya Agamas. S.C Banerji in his book A companion to Tantra cites Paramananda Tantra
In the first chapter, the special feature of this work has been
stated among the different Sundaritantras of the sects, Vaisnava,
Saiva, Saura, Ganapatya, Sakta, etc. Chapter II mentions the number
of sectarian Tantras as follows:
Vaisnava - 6000, Saiva - 10,000, Sakta - 100,000, Ganapatya - 1,000, Saura - 2,000, Bhairava Tantras - 7,000, Yaksa-bhutadi-sadhana - 2,000.
These are the direct verses from Paramananda Tantra Chapter 2:
śṛṇvatra te'mighāsyāmi gaṇanāṃ priye |
ṣaṭsahasrāṇi tantrāṇi vaiṣṇavāni maheśvari ||7||
śaivāni daśasāhasra saṃkhyāni parigaṇyate |
śata sāhasrasankhyāni śāktatantrāṇi vai punaḥ ||8||
gaṇeśasya sahasrāṇi saurāṇi dviguṇāni tu |
madīyāni tu tantrāṇi sapta sāhasrakāṇi vai ||9||
So, these temples where Ganesha is the main deity follow Ganapatya agamas. There are many Tantrik forms of Ganesha worshipped by people. Ganesha existed as an independent god in the history rather than only the obstacle remover. But the people who worshipped Vishvaksena are adherents of Vaishnavism. So, there are no separate temples of Vishwaksena like there are for Ganesha.
But the Ganapatya sect has become very less popular. The main temples where Ganesha is the main deity are constructed by smartas who follow Panchayatana pooja where equal importance is given to all the deities. Hence we see that Lord Shiva, Parvati and others are also given equal importance in the temples even though presided by Ganesha.
These are the reasons Vishvaksena doesn't have temples dedicated to him but has a separate shrine included within the premises of Lord Vishnu's temples.