Gods like Shiva, Lakshmi, Vishnu are not there in Vedas and given importance later in Puranas.

The Narayana Sukta is in a way, the appendix to the Purusha-Sukta of the Veda. Here is a verse from that:

nārāyaṇaḥ paraṁ brahma tattvaṁ nārāyaṇaḥ paraḥ,
nārāyaṇaḥ paro jyotirātmā nārāyaṇaḥ paraḥ.
nārāyaṇaḥ paro dhyātā dhyānam nārāyaṇaḥ paraḥ.
The Lord Narayana is the Supreme Absolute; Narayana is the Supreme Reality; Narayana is the Supreme Light; Narayana is the Supreme Self; Narayana is the Supreme Meditator; Narayana is the Supreme Meditation.

It is telling clearly that Narayana (Vishnu) is the paraṁ brahma (meaning Absolute God). If Narayana simply means one of the name of God like Indra, Rudra etc, still it is not easy to translate it.

We also note in the Rig Veda that, just as Indra’s avatar in later times (Arjuna, the avataar of Indra) is unable to defeat the Kauravas without the help of Vishnu’s avatar Krishna, so in the Rig Veda, Indra must get Vishnu to help him kill the demon, Vritra. He is hence called Indra’s sakha or friend.

Among the Vedas, the Purusha Sukta is held in the highest esteem as it forms an integral part of each of the four Vedas. The Purusha Suktam is seen earliest in the Rg Veda, as the 90th Suktam of its 10th mandalam, with 16 mantrams. Later, it is seen in the Vajasaneyi Samhita of the Shukla Yajur Vedam, the Taittriya Aranyaka of the Krishna Yajur Vedam, the Sama Veda, and the Atharvana Veda, with some modifications. It is also referred to in smrtis, itihasas, puranas and Agamas. It is so named because it extols the pre-eminence of Paramaatma -Sriman Narayana. Take the following verse from Purusha sukta:

From His mind, the Moon was born; from His eye, the Sun;
From His mouth, Indra and Agni were born;
From His breath, the Wind (Vāyu). …13

Hreescha the lakshmischa patnyou.Ahorathre paarswe.
Nakshatrani roopam.Aswinou vyatham. 2-6

Hree and Lakshmi are your wives,
Day and night are your right and left,
The constellation of stars your body,
And Aswini devas your open mouth.

It is clear that Narayana is the actual creator. This is explaining the fact that the creation of this universe is like a yagna (a type of sacrifice) in which Lord has used his shakti or power to create different celestial bodies, planets, material elements, etc. Also different demigods like Indra, Agni, etc were created by Him. When the above verses say that they have been created from different parts of God's body, it is explaining the gigantic glory of God. Here body doesn't mean that God is limited and He is having a physical body like us. It is a spiritual or transcendental body (energy and mass can be converted back and forth) from which this whole world is emanated. This is what Krishna showed in Bhagavad Gita. Vishwaroopa is the form taken by Krishna in the battlefield of Kurukshetra when Arjuna asked him to reveal his true form. In this form, Krishna no longer looks familiar. He is neither cowherd nor charioteer.  He is a magnificent being with countless legs and countless arms and countless heads, breathing fire, containing within himself all the things that exist – all the worlds, all the animate beings and inanimate objects.  Gods headed by Brahma, Rudra, etc was seen this form.

The superior form of energy of the Personality of Godhead is described in the Bhagwat Geeta as Para Prakriti. We belong to this category. We are basically spirits and our consciousness (self itself) is borrowed from God's energy. The inferior energy or the material energy is called Apara Prakriti or material nature  from which this world is created. 

As per Balitha sukta from Rig-Veda (1.141.1-5), Lord Hanuman is told to be an incarnation of Lord Vayu whose second and third incarnations are told to be Bhimasena and Sripad Madhva (yadImanupradivO madhva AdhavE guhasantham.h maatarishvaa mathaayatI) in the same sukta.

Sri Sukta, also called Sri Suktam, is a Sanskrit devotional hymn (set of slokas) revering Sri or Lakshmi, the Hindu goddess of wealth, prosperity and fertility. The hymns are found in the Rig Vedic khilanis, which are appendixes to the Rigveda. Sri-Lakshmi is associated with Vishnu as his wife or consort in this hymns. Those who have read only impersonal aspect of God from Vedas should read this. The Sri Sukta uses the motifs of lotus (padma or kamala) and elephantgaja) – symbols that are consistently linked with the goddess Sri-Lakshmi in Puranas written later. The Sri sukta describes Sri as glorious, ornamented, royal, lustrous as gold, and radiant as fire, moon and the sun. 

The Sri Sukta of the Veda mentions the personal aspects of God in the following verses:

hiraṇyavarṇāṁ hariṇīṁ suvarṇarajatasrajām,

candrāṁ hiraṇmayīṁ lakṣmīṁ jātavedo ma āvaha.

tāṁ ma āvaha jātavedo lakṣmīmanapagāminīm,

yasyāṁ hiraṇyaṁ vindeyaṁ gāmaśvaṁ puruṣānaham.

Invoke for me, O Agni, the Goddess Lakshmi, who shines like gold, yellow in hue, wearing gold and silver garlands, blooming like the moon, the embodiment of wealth. O Agni! Invoke for me that unfailing Lakshmi, being blessed by whom I shall win wealth, cattle, horses and men.

upaitu māṁ devasakhaḥ kīrtiśca maṇinā saha

prādurbhūto’smi rāṣṭre’smin kīrtimṛddhiṁ dadātu me.

kṣutpipāsāmalāṁ jyeṣṭhāmalakṣmīṁ nāśayāmyaham,

abhūtimasamṛddhiṁ ca sarvāṁ nirṇuda me gṛahāt.

O Lakshmi! I am born in this country with the heritage of wealth. May the friend of the Lord Siva (Kubera) and Kirti (fame) come to me. May these (having taken their abode with me) bestow on me fame and prosperity. I shall destroy the elder sister of Lakshmi, the embodiment of inauspiciousness and such evil as hunger, thirst, and the like. O Lakshmi! Drive out from my abode all misfortune and poverty.