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

1. Shaivism (where Shiva is worshipped as supreme)

2. Vaishnavism (where Vishnu is worshipped as supreme)
3. Shaktism (where Shakti is worshipped as Supreme)
4. Ganapatyam (where Ganapati or Ganesha is worshipped as Supreme)
5. 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.